Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167882.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_15, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 22478863
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 61000 characters in sequence are not A, C, G, or T
File 10 of 106
Found at i:1593127 original size:35 final size:35
Alignment explanation
Indices: 1593088--1593210 Score: 93
Period size: 35 Copynumber: 3.5 Consensus size: 35
1593078 GAATCAAAAA
* *
1593088 CCTAAACCCCAAAATCTGAAACTTGAAACCCTACC
1 CCTAAAACCCAAAATCTAAAACTTGAAACCCTACC
* ** * * **** **
1593123 CCTAAAATCCAAAATCTCAAGCCATAAAATAAAAAA
1 CCTAAAACCCAAAATCT-AAAACTTGAAACCCTACC
* *
1593159 CCTAAACCCCAAAATCCAAAACTTGAAACCCTACC
1 CCTAAAACCCAAAATCTAAAACTTGAAACCCTACC
*
1593194 CCTAAAATCCAAAATCT
1 CCTAAAACCCAAAATCT
1593211 TAAGCCCTAA
Statistics
Matches: 58, Mismatches: 29, Indels: 2
0.65 0.33 0.02
Matches are distributed among these distances:
35 37 0.64
36 21 0.36
ACGTcount: A:0.47, C:0.33, G:0.03, T:0.17
Consensus pattern (35 bp):
CCTAAAACCCAAAATCTAAAACTTGAAACCCTACC
Found at i:1593138 original size:71 final size:71
Alignment explanation
Indices: 1593063--1593210 Score: 235
Period size: 71 Copynumber: 2.1 Consensus size: 71
1593053 TCAAAACCTC
* * **
1593063 AAATCTCAAACTC-TAGAATCAAAAACCTAAACCCCAAAATCTGAAACTTGAAACCCTACCCCTA
1 AAATCTCAAAC-CATAAAATAAAAAACCTAAACCCCAAAATCCAAAACTTGAAACCCTACCCCTA
1593127 AAATCCA
65 AAATCCA
*
1593134 AAATCTCAAGCCATAAAATAAAAAACCTAAACCCCAAAATCCAAAACTTGAAACCCTACCCCTAA
1 AAATCTCAAACCATAAAATAAAAAACCTAAACCCCAAAATCCAAAACTTGAAACCCTACCCCTAA
1593199 AATCCA
66 AATCCA
1593205 AAATCT
1 AAATCT
1593211 TAAGCCCTAA
Statistics
Matches: 71, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
70 1 0.01
71 70 0.99
ACGTcount: A:0.49, C:0.30, G:0.03, T:0.18
Consensus pattern (71 bp):
AAATCTCAAACCATAAAATAAAAAACCTAAACCCCAAAATCCAAAACTTGAAACCCTACCCCTAA
AATCCA
Found at i:1593188 original size:28 final size:28
Alignment explanation
Indices: 1593156--1593229 Score: 73
Period size: 28 Copynumber: 2.6 Consensus size: 28
1593146 ATAAAATAAA
1593156 AAACCTAAACCCCAAAATCCAAAA-CTT
1 AAACCTAAACCCCAAAATCCAAAATCTT
1593183 GAAACCCT--ACCCCTAAAATCCAAAATCTT
1 -AAA-CCTAAACCCC-AAAATCCAAAATCTT
* *
1593212 AAGCCCTAAAACCCAAAA
1 AA-ACCTAAACCCCAAAA
1593230 CCTAAAAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
27 5 0.13
28 19 0.50
29 10 0.26
30 4 0.11
ACGTcount: A:0.49, C:0.34, G:0.03, T:0.15
Consensus pattern (28 bp):
AAACCTAAACCCCAAAATCCAAAATCTT
Found at i:1593216 original size:71 final size:71
Alignment explanation
Indices: 1593083--1593222 Score: 244
Period size: 71 Copynumber: 2.0 Consensus size: 71
1593073 CTCTAGAATC
**
1593083 AAAAACCTAAACCCCAAAATCTGAAACTTGAAACCCTACCCCTAAAATCCAAAATCTCAAGCCAT
1 AAAAACCTAAACCCCAAAATCCAAAACTTGAAACCCTACCCCTAAAATCCAAAATCTCAAGCCAT
1593148 AAAATA
66 AAAATA
* *
1593154 AAAAACCTAAACCCCAAAATCCAAAACTTGAAACCCTACCCCTAAAATCCAAAATCTTAAGCCCT
1 AAAAACCTAAACCCCAAAATCCAAAACTTGAAACCCTACCCCTAAAATCCAAAATCTCAAGCCAT
1593219 AAAA
66 AAAA
1593223 CCCAAAACCT
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
71 65 1.00
ACGTcount: A:0.49, C:0.31, G:0.04, T:0.16
Consensus pattern (71 bp):
AAAAACCTAAACCCCAAAATCCAAAACTTGAAACCCTACCCCTAAAATCCAAAATCTCAAGCCAT
AAAATA
Found at i:1598242 original size:305 final size:300
Alignment explanation
Indices: 1597692--1598585 Score: 1087
Period size: 306 Copynumber: 2.9 Consensus size: 300
1597682 TATTCGAAAA
* *
1597692 GATAAATTTTAATGGTTGGATTATTGAAGGCAGTTATATCCAAAATGCCTTCAATAATATTTTGT
1 GATAAATTTTAATGGTTGGATTATTGAAGGCGGTTATATCCAAAATGCCTTCAATAACATTTTGT
** * * * * *
1597757 TAAAAATTATTCAAGGCATTACCCGTAGGAAAATGCCATTCATAATCCATTCAATTAATTTTTAG
66 TAAGGATTATTCAAGGCGTTACCTGTAGGAAAACGCCCTTCATAATCCATTCGATTAATTTTTAG
** * *
1597822 TTGGTATTATTGAAGGTTTTTTTTTAAAACGCCTTCAATAATTTATATAAAAAAAGATGA-GATG
131 TTGGTATTATTGAAGGCATTTTTTTAAAACGCCTTCAATAATTTATA-CAAAAAAGA-CACGATG
* * * * *
1597886 GATTCTTGAAGGCATTTTTTGCCTAAAATGTCTTTAACATTCTATACAATAAATTTTTGAAGGGA
194 GATT-TTGAAGGTATTTTTTGCCTAAAATGCCTTTAATATTCCACACAATAAATTTTTG--GGGA
* * *
1597951 TTATTGAAGGCGATTTTGGTTGAAAATACTATTAATATTTCAGAC
256 TTATTGAAGGCGATTTTGGTTAAAAACACCATTAATATTTCAGAC
* * *
1597996 GATAAATTTTAATTGTTAGATTATTGAAGGCGGTTATATCCAGAAATGCCTTCAATAACATTTTC
1 GATAAATTTTAATGGTTGGATTATTGAAGGCGGTTATATCCA-AAATGCCTTCAATAACATTTTG
* *
1598061 TTAGGGATTATTCAAGGCGTTACCTATAGGAAAACGCCCTTCATAATCCATTCGATTAATTTTTA
65 TTAAGGATTATTCAAGGCGTTACCTGTAGGAAAACGCCCTTCATAATCCATTCGATTAATTTTTA
* * * *
1598126 GTTGATATTATTGAAGGCATTTTCTTAAAATGCCTTCAATAATTTATA-AAAAGAAGACACGACG
130 GTTGGTATTATTGAAGGCATTTTTTTAAAACGCCTTCAATAATTTATACAAAA-AAGACACGATG
* * **
1598190 GATTTTAAAAGTATTTTTTGCCTAAAATGCCTTTAATATTGAAGACACAATAAATTCTTTGTGGG
194 GATTTTGAAGGTATTTTTTGCCTAAAATGCCTTTAATATT--CCACACAATAAATT-TTTG-GGG
* * * *
1598255 ATTATTGAAGGTGATTTTGGTAAAAGAACGCCATTAATATTTCAGAT
255 ATTATTGAAGGCGATTTTGGTTAAA-AACACCATTAATATTTCAGAC
* **
1598302 GATAAATTTTAATGGTTGGATTATTGAAGGTGGTTATATCCATAAACACCTTCAATAACATTTTG
1 GATAAATTTTAATGGTTGGATTATTGAAGGCGGTTATATCCA-AAATGCCTTCAATAACATTTTG
* * * *
1598367 TTAAGGATTATTCAAGGCGTTACTTGTAAGAAAACACCCTTCATAATCCATTTGATTAATTTTTA
65 TTAAGGATTATTCAAGGCGTTACCTGTAGGAAAACGCCCTTCATAATCCATTCGATTAATTTTTA
* * ** * * *
1598432 GTTGGTATTATT-ATA-GCTGTTTTTTTAAAACACCTTCAATAATCCATACATAAAAGGCGCGAT
130 GTTGGTATTATTGA-AGGC-ATTTTTTTAAAACGCCTTCAATAATTTATACAAAAAAGACACGAT
* * * *
1598495 GAATTTTTGAAGGTATTTTTT-CCCAAAATGCCTTTAATATTCCACATAATTAATTTTTGGGTGA
193 GGA-TTTTGAAGGTATTTTTTGCCTAAAATGCCTTTAATATTCCACACAATAAATTTTTGGG-GA
*
1598559 TTATTGAAGGCGGTTTTGGTTAAAAAC
256 TTATTGAAGGCGATTTTGGTTAAAAAC
1598586 GCCTTCAAAA
Statistics
Matches: 506, Mismatches: 72, Indels: 26
0.84 0.12 0.04
Matches are distributed among these distances:
302 5 0.01
303 63 0.12
304 60 0.12
305 158 0.31
306 202 0.40
307 18 0.04
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (300 bp):
GATAAATTTTAATGGTTGGATTATTGAAGGCGGTTATATCCAAAATGCCTTCAATAACATTTTGT
TAAGGATTATTCAAGGCGTTACCTGTAGGAAAACGCCCTTCATAATCCATTCGATTAATTTTTAG
TTGGTATTATTGAAGGCATTTTTTTAAAACGCCTTCAATAATTTATACAAAAAAGACACGATGGA
TTTTGAAGGTATTTTTTGCCTAAAATGCCTTTAATATTCCACACAATAAATTTTTGGGGATTATT
GAAGGCGATTTTGGTTAAAAACACCATTAATATTTCAGAC
Found at i:1603818 original size:16 final size:16
Alignment explanation
Indices: 1603772--1603818 Score: 60
Period size: 15 Copynumber: 3.0 Consensus size: 16
1603762 AGAGAAAATC
*
1603772 CTTTAATTTTCTAGCA
1 CTTTAATTTTCTTGCA
*
1603788 C-TTAATTTTCATGCA
1 CTTTAATTTTCTTGCA
*
1603803 CTTTAAGTTTCTTGCA
1 CTTTAATTTTCTTGCA
1603819 ATGTAATTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.23, C:0.19, G:0.09, T:0.49
Consensus pattern (16 bp):
CTTTAATTTTCTTGCA
Found at i:1611148 original size:3 final size:3
Alignment explanation
Indices: 1611140--1611172 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
1611130 ATTTTTAATT
1611140 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1611173 ATATATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1621866 original size:16 final size:16
Alignment explanation
Indices: 1621845--1621879 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1621835 GCCAACATAA
*
1621845 CATGCATTGAATTTTG
1 CATGCATTGAATTTCG
*
1621861 CATGCATTGCATTTCG
1 CATGCATTGAATTTCG
1621877 CAT
1 CAT
1621880 AGTATATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.40
Consensus pattern (16 bp):
CATGCATTGAATTTCG
Found at i:1622203 original size:41 final size:42
Alignment explanation
Indices: 1622146--1622237 Score: 109
Period size: 41 Copynumber: 2.3 Consensus size: 42
1622136 ATAGAAGATG
* * *
1622146 AATTTACTTTTAAAAGTTGTAG-TGCCTCTATTTAGAGGAGC
1 AATTTACTTTCAAAAGTCGTAGTTACCTCTATTTAGAGGAGC
* * *
1622187 AATTTGCTTTCAAAAGTCGTGGTTACCTCTGTTTAGAGGAGC
1 AATTTACTTTCAAAAGTCGTAGTTACCTCTATTTAGAGGAGC
1622229 -ATTTA-TTTC
1 AATTTACTTTC
1622238 TTTAAAAGTT
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
40 4 0.09
41 22 0.51
42 17 0.40
ACGTcount: A:0.26, C:0.14, G:0.20, T:0.40
Consensus pattern (42 bp):
AATTTACTTTCAAAAGTCGTAGTTACCTCTATTTAGAGGAGC
Found at i:1622223 original size:42 final size:40
Alignment explanation
Indices: 1622170--1622333 Score: 125
Period size: 42 Copynumber: 3.9 Consensus size: 40
1622160 AGTTGTAGTG
* *
1622170 CCTCTATTTAGAGGAGCAATTTGCTTTCAAAAGTCGTGGTTA
1 CCTCTGTTTAGAGGAGCAATTT-CTTT-AAAAGTCATGGTTA
* *
1622212 CCTCTGTTTAGAGGAGCATTTATTTCTTTAAAAGTTATGGTTG
1 CCTCTGTTTAGAGGAGCA---ATTTCTTTAAAAGTCATGGTTA
* * * * *
1622255 CTTCTGTTTAGAGGAGTAATTTATTTTTAAAAATTATGG--A
1 CCTCTGTTTAGAGGAGCAA-TT-TCTTTAAAAGTCATGGTTA
*
1622295 GCCTCTGTTTAGAGGAGCTTTTATTTCTTTAAAAGTCAT
1 -CCTCTGTTTAGAGGAGC---AATTTCTTTAAAAGTCAT
1622334 TGAGCCTCTG
Statistics
Matches: 98, Mismatches: 15, Indels: 18
0.75 0.11 0.14
Matches are distributed among these distances:
40 1 0.01
41 17 0.17
42 42 0.43
43 29 0.30
44 5 0.05
45 4 0.04
ACGTcount: A:0.26, C:0.12, G:0.20, T:0.42
Consensus pattern (40 bp):
CCTCTGTTTAGAGGAGCAATTTCTTTAAAAGTCATGGTTA
Found at i:1622339 original size:42 final size:42
Alignment explanation
Indices: 1622212--1622444 Score: 177
Period size: 42 Copynumber: 5.4 Consensus size: 42
1622202 GTCGTGGTTA
* *
1622212 CCTCTGTTTAGAGGAGC-ATTTATTTCTTTAAAAGTTATGGTTG
1 CCTCTGTTTAGAGGAGCTATTTATTT-TTTAAAAGTTATTG-AG
* * *
1622255 CTTCTGTTTAGAGGAG-TAATTTA-TTTTTAAAAATTATGGAG
1 CCTCTGTTTAGAGGAGCT-ATTTATTTTTTAAAAGTTATTGAG
*
1622296 CCTCTGTTTAGAGGAGCT-TTTATTTCTTTAAAAGTCATTGAG
1 CCTCTGTTTAGAGGAGCTATTTATTT-TTTAAAAGTTATTGAG
* * * * * *
1622338 CCTCTGCTTCGAAGAGCTTTGTTTATTTTTTTAAAAGTTGTTGAA
1 CCTCTGTTTAGAGGAGC--TATTTA-TTTTTTAAAAGTTATTGAG
* * * * * **
1622383 CCTCTGATTAGATGAGTTTTGTTTATTTTTTCAAAGTCGTTGAG
1 CCTCTGTTTAGAGGAG--CTATTTATTTTTTAAAAGTTATTGAG
*
1622427 CCTCTGTTTAGAAGAGCT
1 CCTCTGTTTAGAGGAGCT
1622445 TTGATCAAAA
Statistics
Matches: 156, Mismatches: 23, Indels: 23
0.77 0.11 0.11
Matches are distributed among these distances:
40 4 0.03
41 18 0.12
42 42 0.27
43 17 0.11
44 36 0.23
45 36 0.23
46 3 0.02
ACGTcount: A:0.24, C:0.12, G:0.20, T:0.44
Consensus pattern (42 bp):
CCTCTGTTTAGAGGAGCTATTTATTTTTTAAAAGTTATTGAG
Found at i:1622375 original size:45 final size:45
Alignment explanation
Indices: 1622293--1622447 Score: 174
Period size: 45 Copynumber: 3.5 Consensus size: 45
1622283 AAAAATTATG
* * * *
1622293 GAGCCTCTGTTTAGAGGAGC--T-TTTATTTCTTTAAAAGTCATT
1 GAGCCTCTGATTAGAAGAGCTTTGTTTATTTTTTTAAAAGTCGTT
* * *
1622335 GAGCCTCTGCTTCGAAGAGCTTTGTTTATTTTTTTAAAAGTTGTT
1 GAGCCTCTGATTAGAAGAGCTTTGTTTATTTTTTTAAAAGTCGTT
* * * *
1622380 GAACCTCTGATTAGATGAGTTTTGTTTA-TTTTTTCAAAGTCGTT
1 GAGCCTCTGATTAGAAGAGCTTTGTTTATTTTTTTAAAAGTCGTT
*
1622424 GAGCCTCTGTTTAGAAGAGCTTTG
1 GAGCCTCTGATTAGAAGAGCTTTG
1622448 ATCAAAATTT
Statistics
Matches: 93, Mismatches: 17, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
42 17 0.18
44 35 0.38
45 41 0.44
ACGTcount: A:0.22, C:0.14, G:0.21, T:0.44
Consensus pattern (45 bp):
GAGCCTCTGATTAGAAGAGCTTTGTTTATTTTTTTAAAAGTCGTT
Found at i:1622486 original size:11 final size:10
Alignment explanation
Indices: 1622470--1622510 Score: 55
Period size: 11 Copynumber: 3.9 Consensus size: 10
1622460 ACCAAAACAA
1622470 AAAAACAAAAC
1 AAAAA-AAAAC
1622481 AAAAACAAAAC
1 AAAAA-AAAAC
*
1622492 AAAAAAAAGC
1 AAAAAAAAAC
1622502 AAAAAAAAA
1 AAAAAAAAA
1622511 TATCGAGTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
10 12 0.43
11 16 0.57
ACGTcount: A:0.85, C:0.12, G:0.02, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:1622505 original size:6 final size:5
Alignment explanation
Indices: 1622462--1622509 Score: 50
Period size: 5 Copynumber: 10.0 Consensus size: 5
1622452 AAATTTTAAC
1622462 CAAAA C-AAA -AAAA CAAAA CAAAAA CAAAA CAAAA -AAAA GCAAAA -AAAA
1 CAAAA CAAAA CAAAA CAAAA C-AAAA CAAAA CAAAA CAAAA -CAAAA CAAAA
1622510 ATATCGAGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
4 14 0.37
5 15 0.39
6 9 0.24
ACGTcount: A:0.83, C:0.15, G:0.02, T:0.00
Consensus pattern (5 bp):
CAAAA
Found at i:1622695 original size:3 final size:3
Alignment explanation
Indices: 1622687--1622762 Score: 68
Period size: 3 Copynumber: 24.7 Consensus size: 3
1622677 ATTTTTAATT
* *
1622687 TTA TTA TTA TTA TTA TTA TTAA TT- TTA TTA TAA TTA TTTA TAA TTA
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA -TTA TTA TTA
1622733 TTTA TTTA TTTA TT- TT- TTA TTA TTA TTA TT
1 -TTA -TTA -TTA TTA TTA TTA TTA TTA TTA TT
1622763 TTTTTTATAT
Statistics
Matches: 64, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
2 6 0.09
3 41 0.64
4 17 0.27
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1622708 original size:24 final size:24
Alignment explanation
Indices: 1622681--1622770 Score: 81
Period size: 24 Copynumber: 3.5 Consensus size: 24
1622671 AATTTAATTT
1622681 TTAATTTTATTATTATTATTATTA
1 TTAATTTTATTATTATTATTATTA
* *
1622705 TTAATTTTATTATAATTATTTATAA
1 TTAATTTTATTATTATTA-TTATTA
* *
1622730 TTATTTATTTATTTATTTTTTATTATTA
1 TTA-AT-TTTA-TTA-TTATTATTATTA
* *
1622758 TTATTTTTTTTAT
1 TTAATTTTATTAT
1622771 ATTTTTTGGT
Statistics
Matches: 54, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
24 18 0.33
25 11 0.20
26 4 0.07
27 6 0.11
28 11 0.20
29 4 0.07
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (24 bp):
TTAATTTTATTATTATTATTATTA
Found at i:1622729 original size:10 final size:10
Alignment explanation
Indices: 1622714--1622745 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
1622704 ATTAATTTTA
1622714 TTATAATTAT
1 TTATAATTAT
1622724 TTATAATTAT
1 TTATAATTAT
1622734 TTAT--TTAT
1 TTATAATTAT
1622742 TTAT
1 TTAT
1622746 TTTTTATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.36
10 14 0.64
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (10 bp):
TTATAATTAT
Found at i:1622737 original size:14 final size:13
Alignment explanation
Indices: 1622672--1622763 Score: 58
Period size: 12 Copynumber: 7.3 Consensus size: 13
1622662 TCTAATTTTA
1622672 ATTTA-ATT-TTT
1 ATTTATATTATTT
1622683 AATTT-TATTA-TT
1 -ATTTATATTATTT
*
1622695 A-TTATTATTATTA
1 ATTTA-TATTATTT
1622708 ATTT-TATTATAATT
1 ATTTATATTAT--TT
1622722 ATTTATAATTATTT
1 ATTTAT-ATTATTT
1622736 ATTTAT-TTATTT
1 ATTTATATTATTT
1622748 -TTTATTATTA-TT
1 ATTTA-TATTATTT
1622760 ATTT
1 ATTT
1622764 TTTTTATATT
Statistics
Matches: 65, Mismatches: 2, Indels: 25
0.71 0.02 0.27
Matches are distributed among these distances:
10 2 0.03
11 5 0.08
12 29 0.45
13 8 0.12
14 15 0.23
15 1 0.02
16 5 0.08
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
ATTTATATTATTT
Found at i:1622766 original size:18 final size:18
Alignment explanation
Indices: 1622693--1622770 Score: 68
Period size: 18 Copynumber: 4.2 Consensus size: 18
1622683 AATTTTATTA
**
1622693 TTATTATTATTATTAATT
1 TTATTATTATTATTTTTT
* **
1622711 TTATTATAATTATTTATAA
1 TTATTATTATTATTT-TTT
*
1622730 TTATTTATTTATT-TATTTT
1 TTA-TTA-TTATTATTTTTT
1622749 TTATTATTATTATTTTTT
1 TTATTATTATTATTTTTT
1622767 TTAT
1 TTAT
1622771 ATTTTTTGGT
Statistics
Matches: 46, Mismatches: 10, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
17 5 0.11
18 25 0.54
19 7 0.15
20 5 0.11
21 4 0.09
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TTATTATTATTATTTTTT
Found at i:1622776 original size:28 final size:27
Alignment explanation
Indices: 1622677--1622777 Score: 98
Period size: 25 Copynumber: 3.7 Consensus size: 27
1622667 TTTTAATTTA
*
1622677 ATTTTTAATTTTATTATTATTATTATTATT
1 ATTTTT-ATTATATT-TT-TTATTATTATT
* * *
1622707 AATTTTATTATAATTATTTATAATTATT
1 ATTTTTATTAT-ATTTTTTATTATTATT
*
1622735 -TATTTATT-TATTTTTTATTATTATT
1 ATTTTTATTATATTTTTTATTATTATT
*
1622760 ATTTTTTTTATATTTTTT
1 ATTTTTATTATATTTTTT
1622778 GGTTTGGTTT
Statistics
Matches: 58, Mismatches: 10, Indels: 9
0.75 0.13 0.12
Matches are distributed among these distances:
25 14 0.24
26 7 0.12
27 14 0.24
28 10 0.17
29 5 0.09
30 8 0.14
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (27 bp):
ATTTTTATTATATTTTTTATTATTATT
Found at i:1623755 original size:59 final size:59
Alignment explanation
Indices: 1623690--1624102 Score: 238
Period size: 59 Copynumber: 6.8 Consensus size: 59
1623680 TTTAAAAAAT
1623690 AAAAAAATAATTTTAAGAAAAAGTTGAAAGTATCAATTTTT-TTCGAAAATAAAATTTAA
1 AAAAAAATAATTTTAAGAAAAAGTTGAAAGTATCAATTTTTCTT-GAAAATAAAATTTAA
* * * * **
1623749 GGAAAAAAT-ATTTTGAAG-GAAAGTTGAATA-TATCAA-TTTCCTTTGAACATAAAAATTTCC
1 -AAAAAAATAATTTT-AAGAAAAAGTTGAA-AGTATCAATTTTTC-TTGAAAAT-AAAATTTAA
** * * * *
1623809 AAAAGCAT--TTTGAAG-GAAAGTTGAAAATATCAATTTTTCTTAAAAATAAAATTTCTAAA
1 AAAAAAATAATTTTAAGAAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAAA-TT-T-AA
* ** * *
1623868 ATAAAAATTATCAAGAAAAGTATTTTGAAAAAAAGTTGAAGGTATCAATTTTTCTTGAAATTAAA
1 A-AAAAA--AT------AA-TTTTAAGAA--AAAGTTGAAAGTATCAATTTTTCTTGAAAATAAA
*
1623933 ACTT-A
54 ATTTAA
* * * * *
1623938 AAAAAAAT-ATTTTGAGAAAAAATTAAAAATATCAATTTTTCTTGAAATTAAAATTTCAAA
1 AAAAAAATAATTTTAAGAAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAAATTT--AA
* * * * *
1623998 AAAAAAAAACATTTTGAGAAAAAGTTGAAAGTACCAATTTTTCTTAAAAATAAAATTATCA
1 AAAAAAATA-ATTTTAAGAAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAAATT-TAA
* *
1624059 AGAAAAA-CATTTTAA-AGAAAAGTTGAAAGTATCAATTTTTCTTG
1 AAAAAAATAATTTTAAGA-AAAAGTTGAAAGTATCAATTTTTCTTG
1624103 TACAAAAGCA
Statistics
Matches: 273, Mismatches: 48, Indels: 65
0.71 0.12 0.17
Matches are distributed among these distances:
56 5 0.02
57 60 0.22
58 12 0.04
59 68 0.25
60 32 0.12
61 7 0.03
62 43 0.16
63 1 0.00
67 2 0.01
69 5 0.02
70 2 0.01
71 3 0.01
72 1 0.00
73 1 0.00
74 31 0.11
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (59 bp):
AAAAAAATAATTTTAAGAAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAAATTTAA
Found at i:1623858 original size:57 final size:56
Alignment explanation
Indices: 1623758--1623868 Score: 152
Period size: 57 Copynumber: 2.0 Consensus size: 56
1623748 AGGAAAAAAT
* * *
1623758 ATTTTGAAGGAAAGTTGAATATATCAATTTCCTTTGAACATAAAAATTTCCAAAAGC
1 ATTTTGAAGGAAAGTTGAAAATATCAATTTCCTTTAAAAAT-AAAATTTCCAAAAGC
* *
1623815 ATTTTGAAGGAAAGTTGAAAATATCAATTT-TTCTTAAAAATAAAATTTCTAAAA
1 ATTTTGAAGGAAAGTTGAAAATATCAATTTCCT-TTAAAAATAAAATTTCCAAAA
1623869 TAAAAATTAT
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
56 13 0.27
57 35 0.73
ACGTcount: A:0.45, C:0.09, G:0.11, T:0.35
Consensus pattern (56 bp):
ATTTTGAAGGAAAGTTGAAAATATCAATTTCCTTTAAAAATAAAATTTCCAAAAGC
Found at i:1623893 original size:131 final size:131
Alignment explanation
Indices: 1623752--1624005 Score: 289
Period size: 131 Copynumber: 1.9 Consensus size: 131
1623742 AATTTAAGGA
** * *** *
1623752 AAAAATATTTTGAAGGAAAGTTGAATATATCAATTTC-CTTTGAACA-TAAAAATTTCCAAAAGC
1 AAAAATATTTTGAAAAAAAGTTGAAGATATCAATTTCTC-TTGAA-ATTAAAAATTAAAAAAAAC
* * * * *
1623815 ATTTTGA-AGGAAAGTTGAAAATATCAATTTTTCTTAAAAATAAAATTTCTAAAATAAAAATTAT
64 ATTTTGAGA-AAAAATTAAAAATATCAATTTTTCTTAAAAATAAAATTTCAAAAAAAAAAATTAT
1623879 CAAG
128 CAAG
* * * * *
1623883 AAAAGTATTTTGAAAAAAAGTTGAAGGTATCAATTTTTCTTGAAATTAAAACTTAAAAAAAATAT
1 AAAAATATTTTGAAAAAAAGTTGAAGATATCAATTTCTCTTGAAATTAAAAATTAAAAAAAACAT
* *
1623948 TTTGAGAAAAAATTAAAAATATCAATTTTTCTTGAAATTAAAATTTCAAAAAAAAAAA
66 TTTGAGAAAAAATTAAAAATATCAATTTTTCTTAAAAATAAAATTTCAAAAAAAAAAA
1624006 ACATTTTGAG
Statistics
Matches: 101, Mismatches: 19, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
130 1 0.01
131 98 0.97
132 2 0.02
ACGTcount: A:0.51, C:0.07, G:0.09, T:0.33
Consensus pattern (131 bp):
AAAAATATTTTGAAAAAAAGTTGAAGATATCAATTTCTCTTGAAATTAAAAATTAAAAAAAACAT
TTTGAGAAAAAATTAAAAATATCAATTTTTCTTAAAAATAAAATTTCAAAAAAAAAAATTATCAA
G
Found at i:1623950 original size:57 final size:56
Alignment explanation
Indices: 1623889--1624102 Score: 234
Period size: 62 Copynumber: 3.6 Consensus size: 56
1623879 CAAGAAAAGT
* *
1623889 ATTTTGAAAAAAAGTTGAAGGTATCAATTTTTCTTGAAATTAAAACTTAAAAAAAAT
1 ATTTTGAAAAAAAGTTGAAAGTATCAATTTTTCTTGAAATTAAAA-TTAAAAAAAAC
* *
1623946 ATTTTGAGAAAAAA-TTAAAAATATCAATTTTTCTTGAAATTAAAATTTCAAAAAAAAAAAAC
1 ATTTTGA-AAAAAAGTTGAAAGTATCAATTTTTCTTGAAATTAAAA-TT-----AAAAAAAAC
* * * *
1624008 ATTTTGAGAAAAAGTTGAAAGTACCAATTTTTCTTAAAAATAAAATTATCAAGAAAAAC
1 ATTTTGAAAAAAAGTTGAAAGTATCAATTTTTCTTGAAATTAAAATTA--AA-AAAAAC
1624067 ATTTT-AAAGAAAAGTTGAAAGTATCAATTTTTCTTG
1 ATTTTGAAA-AAAAGTTGAAAGTATCAATTTTTCTTG
1624103 TACAAAAGCA
Statistics
Matches: 132, Mismatches: 14, Indels: 20
0.80 0.08 0.12
Matches are distributed among these distances:
56 1 0.01
57 37 0.28
58 10 0.08
59 36 0.27
61 7 0.05
62 41 0.31
ACGTcount: A:0.50, C:0.07, G:0.09, T:0.34
Consensus pattern (56 bp):
ATTTTGAAAAAAAGTTGAAAGTATCAATTTTTCTTGAAATTAAAATTAAAAAAAAC
Found at i:1624036 original size:62 final size:59
Alignment explanation
Indices: 1623865--1624102 Score: 250
Period size: 57 Copynumber: 4.0 Consensus size: 59
1623855 TAAAATTTCT
* ** * *
1623865 AAAATAAAAATTATCAAGAAAAGTATTTTGAAAAAAAGTTGAAGGTATCAATTTTTCTTG
1 AAAAT-AAAATTATCAAAAAAAACATTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTG
* * * * * *
1623925 AAATTAAAACT-T-AAAAAAAATATTTTGAGAAAAAATTAAAAATATCAATTTTTCTTG
1 AAAATAAAATTATCAAAAAAAACATTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTG
* * *
1623982 AAATTAAAATT-TCAAAAAAAAAAAACATTTTGAGAAAAAGTTGAAAGTACCAATTTTTCTTA
1 AAAATAAAATTATC----AAAAAAAACATTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTG
* *
1624044 AAAATAAAATTATCAAGAAAAACATTTT-AAAGAAAAGTTGAAAGTATCAATTTTTCTTG
1 AAAATAAAATTATCAAAAAAAACATTTTGAGA-AAAAGTTGAAAGTATCAATTTTTCTTG
1624103 TACAAAAGCA
Statistics
Matches: 150, Mismatches: 21, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
57 49 0.33
58 3 0.02
59 43 0.29
60 4 0.03
62 49 0.33
63 2 0.01
ACGTcount: A:0.52, C:0.06, G:0.09, T:0.33
Consensus pattern (59 bp):
AAAATAAAATTATCAAAAAAAACATTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTG
Found at i:1624204 original size:5 final size:5
Alignment explanation
Indices: 1624166--1624203 Score: 60
Period size: 5 Copynumber: 7.6 Consensus size: 5
1624156 TGAATAATTA
1624166 TTTAT TTTAT TTTAT TTTAT TTTATT TTTAT TTT-T TTT
1 TTTAT TTTAT TTTAT TTTAT TTTA-T TTTAT TTTAT TTT
1624204 TGAAACTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
4 4 0.12
5 23 0.72
6 5 0.16
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (5 bp):
TTTAT
Found at i:1630943 original size:23 final size:25
Alignment explanation
Indices: 1630895--1630939 Score: 60
Period size: 23 Copynumber: 1.9 Consensus size: 25
1630885 TTTAAAAACT
*
1630895 AAAAATAATATAAAGATTATTTATA
1 AAAAATAATATAAAGATTATTAATA
1630920 AAAAAT-AT-TAAAGA-TATTAA
1 AAAAATAATATAAAGATTATTAA
1630940 ATAATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 5 0.26
23 6 0.32
24 2 0.11
25 6 0.32
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (25 bp):
AAAAATAATATAAAGATTATTAATA
Found at i:1630972 original size:230 final size:233
Alignment explanation
Indices: 1630384--1630985 Score: 854
Period size: 240 Copynumber: 2.6 Consensus size: 233
1630374 TAGTATTTGC
* * * *
1630384 ATATTTTTTTTCACATT-TTTTATGAAATATATTTAAAAATTGAAGATAATACAATGATTATTTA
1 ATATATTTTTTCACATTCCTTTGTGAAATATATTTAAAAATTGAAGATAATATAATGATTATTTA
* *
1630448 TAAAAATTATTAAAGATATTAAATAATATTTTTAAAAGTTATGATAAATTTAAATACTCATGTTA
66 TAAAAAATATTAAAGATATTAAATAATATTTTTAAAAGTTGTGATAAATTTAAATACTCATGTTA
* * *
1630513 ACTGTAAATAAAGTGAAAAAGATAAATTACTTTAAAATTGGTTTTAAATTGAAATAAAGTAATGT
131 ACTGCAAATAAAGTGAAAAAGAAAAATTACTTTAAAATTGATTTTAAATTGAAATAAAGTAATGT
* *
1630578 ACAAGAGAAACTTTTCTAAAGTTGTTTTGGTATTTATATAT
196 ACAAGAGAAACTTTTCTAAAGTTATTCTGG---TTATATAT
* * *
1630619 ATATATATATATTTCACATTTCCTTTGTGAAATATATTTAAAAGTTGAAGATAATGTAATGAATA
1 ATATAT-T-T-TTTCACA-TTCCTTTGTGAAATATATTTAAAAATTGAAGATAATATAATGATTA
*
1630684 TTTATAAAAAATATTAAAGATATTAAATAATATTTTTAAAAGTTGTGATAAATTTAAATACTTAT
62 TTTATAAAAAATATTAAAGATATTAAATAATATTTTTAAAAGTTGTGATAAATTTAAATACTCAT
* * * * * *
1630749 GTTAATTGCAAATAAATTGAAAAAGAAAAATTATTTTAAAATTGATTTTAAATTGAGATAAGGTG
127 GTTAACTGCAAATAAAGTGAAAAAGAAAAATTACTTTAAAATTGATTTTAAATTGAAATAAAGTA
* *
1630814 ATGTAGATGAGAAAC-TTTCTTAAAGTTATTCTGG-TAT-T-T
192 ATGTACAAGAGAAACTTTTC-TAAAGTTATTCTGGTTATATAT
* * * *
1630853 ATATATTTTTTCACATTCCTTTGTGAAATATATTTAAAAACTAAAAATAATATAAAGATTATTTA
1 ATATATTTTTTCACATTCCTTTGTGAAATATATTTAAAAATTGAAGATAATATAATGATTATTTA
1630918 TAAAAAATATTAAAGATATTAAATAATATTTTTAAAAGTTGTGATAAATTTAAATACTCATGTTA
66 TAAAAAATATTAAAGATATTAAATAATATTTTTAAAAGTTGTGATAAATTTAAATACTCATGTTA
1630983 ACT
131 ACT
1630986 TTAGATAAAT
Statistics
Matches: 329, Mismatches: 32, Indels: 17
0.87 0.08 0.04
Matches are distributed among these distances:
230 109 0.33
231 7 0.02
232 1 0.00
233 1 0.00
234 7 0.02
235 6 0.02
236 4 0.01
237 1 0.00
238 7 0.02
239 6 0.02
240 180 0.55
ACGTcount: A:0.45, C:0.04, G:0.10, T:0.41
Consensus pattern (233 bp):
ATATATTTTTTCACATTCCTTTGTGAAATATATTTAAAAATTGAAGATAATATAATGATTATTTA
TAAAAAATATTAAAGATATTAAATAATATTTTTAAAAGTTGTGATAAATTTAAATACTCATGTTA
ACTGCAAATAAAGTGAAAAAGAAAAATTACTTTAAAATTGATTTTAAATTGAAATAAAGTAATGT
ACAAGAGAAACTTTTCTAAAGTTATTCTGGTTATATAT
Found at i:1631104 original size:20 final size:21
Alignment explanation
Indices: 1631043--1631110 Score: 68
Period size: 23 Copynumber: 3.2 Consensus size: 21
1631033 TACAAGAGAA
* *
1631043 ATTTCATTAAAATTTAAATTATT
1 ATTTGATTAAATTTTAAA-TA-T
*
1631066 TTTTGATTAAATTTTAAATA-
1 ATTTGATTAAATTTTAAATAT
1631086 ATTTGA-TAAATTTTAAAATAT
1 ATTTGATTAAATTTT-AAATAT
1631107 ATTT
1 ATTT
1631111 TTAATAAATA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
19 8 0.21
20 10 0.26
21 4 0.10
22 2 0.05
23 15 0.38
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (21 bp):
ATTTGATTAAATTTTAAATAT
Found at i:1631118 original size:23 final size:23
Alignment explanation
Indices: 1631050--1631129 Score: 62
Period size: 23 Copynumber: 3.6 Consensus size: 23
1631040 GAAATTTCAT
* * *
1631050 TAAAATTTAAATTAT-TTTTTGAT
1 TAAATTTTAAAATATATTTTT-AA
*
1631073 TAAATTTT-AAATA-A--TTTGA
1 TAAATTTTAAAATATATTTTTAA
1631092 TAAATTTTAAAATATATTTTTAA
1 TAAATTTTAAAATATATTTTTAA
1631115 TAAATAATTTAAAAT
1 TAAAT--TTTAAAAT
1631130 TAATAAATAT
Statistics
Matches: 45, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
19 8 0.18
20 8 0.18
21 1 0.02
22 4 0.09
23 16 0.36
25 8 0.18
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (23 bp):
TAAATTTTAAAATATATTTTTAA
Found at i:1632557 original size:34 final size:34
Alignment explanation
Indices: 1632514--1632579 Score: 116
Period size: 34 Copynumber: 1.9 Consensus size: 34
1632504 ATGTTTGGTT
1632514 GACATTAATAAAC-CAAAGTCAACTTCAAGGCTTG
1 GACATTAATAAACAC-AAGTCAACTTCAAGGCTTG
1632548 GACATTAATAAACACAAGTCAACTTCAAGGCT
1 GACATTAATAAACACAAGTCAACTTCAAGGCT
1632580 CGGCTTTCTG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
34 30 0.97
35 1 0.03
ACGTcount: A:0.42, C:0.21, G:0.14, T:0.23
Consensus pattern (34 bp):
GACATTAATAAACACAAGTCAACTTCAAGGCTTG
Found at i:1633047 original size:15 final size:14
Alignment explanation
Indices: 1633029--1633080 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 14
1633019 TAGGATATGC
1633029 AATTATATTATATAT
1 AATTATA-TATATAT
1633044 AATTATATATATAATT
1 AATTATATATAT-A-T
1633060 CAATTATATATAATAT
1 -AATTATATAT-ATAT
1633076 AATTA
1 AATTA
1633081 ATAAATTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
14 5 0.15
15 13 0.39
16 2 0.06
17 11 0.33
18 2 0.06
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (14 bp):
AATTATATATATAT
Found at i:1633067 original size:23 final size:21
Alignment explanation
Indices: 1633035--1633094 Score: 56
Period size: 20 Copynumber: 2.9 Consensus size: 21
1633025 ATGCAATTAT
1633035 ATTATATATAATTATATATATA
1 ATTA-ATATAATTATATATATA
1633057 ATTCAAT-T-A-TATATAATATA
1 ATT-AATATAATTATAT-ATATA
*
1633077 ATTAATA-AATTTTATATA
1 ATTAATATAATTATATATA
1633095 AAAAATAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 12
0.71 0.02 0.27
Matches are distributed among these distances:
19 8 0.25
20 13 0.41
21 5 0.16
22 5 0.16
23 1 0.03
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (21 bp):
ATTAATATAATTATATATATA
Found at i:1633120 original size:24 final size:25
Alignment explanation
Indices: 1633083--1633133 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 25
1633073 TATAATTAAT
*
1633083 AAATTTTATATAAAA-AATAAAAAA
1 AAATTTAATATAAAATAATAAAAAA
*
1633107 AAATTTAATGTAAAATAATAAAAAA
1 AAATTTAATATAAAATAATAAAAAA
1633132 AA
1 AA
1633134 TTAAAAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 13 0.54
25 11 0.46
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (25 bp):
AAATTTAATATAAAATAATAAAAAA
Found at i:1633708 original size:19 final size:21
Alignment explanation
Indices: 1633684--1633722 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1633674 ATATTGAAAC
*
1633684 TGAATA-G-ATAAATAAAGTA
1 TGAATATGCATAAAAAAAGTA
1633703 TGAATATGCATAAAAAAAGT
1 TGAATATGCATAAAAAAAGT
1633723 GAATAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 1 0.06
21 10 0.59
ACGTcount: A:0.56, C:0.03, G:0.15, T:0.26
Consensus pattern (21 bp):
TGAATATGCATAAAAAAAGTA
Found at i:1635062 original size:44 final size:45
Alignment explanation
Indices: 1634968--1635062 Score: 131
Period size: 44 Copynumber: 2.2 Consensus size: 45
1634958 ACCCATATAC
* * *
1634968 ATAAAATCTAATATTATAATGTATGATTAATTTTATAACAAAAAT
1 ATAAAATCTAACATTATAATGTATCATTAATCTTATAACAAAAAT
* *
1635013 A-AAAATCTAACATTATAATGTATCATTAATCTTAT-ATAAATAT
1 ATAAAATCTAACATTATAATGTATCATTAATCTTATAACAAAAAT
1635056 ATAAAAT
1 ATAAAAT
1635063 TATTATATTA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
43 7 0.16
44 36 0.82
45 1 0.02
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.39
Consensus pattern (45 bp):
ATAAAATCTAACATTATAATGTATCATTAATCTTATAACAAAAAT
Found at i:1639539 original size:12 final size:13
Alignment explanation
Indices: 1639501--1639540 Score: 57
Period size: 12 Copynumber: 3.2 Consensus size: 13
1639491 TGCATTTGTT
1639501 TTTTTATTTATT-
1 TTTTTATTTATTA
*
1639513 TATTTATTTATTA
1 TTTTTATTTATTA
1639526 TTTTTATTT-TTA
1 TTTTTATTTATTA
1639538 TTT
1 TTT
1639541 AAATATTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 17 0.68
13 8 0.32
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTATTTATTA
Found at i:1639567 original size:21 final size:22
Alignment explanation
Indices: 1639543--1639589 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1639533 TTTTATTTAA
1639543 ATATTT-TTAAATAACATCA-TT
1 ATATTTATTAAATAA-ATCATTT
*
1639564 ATATTTATTTAATAAATCATTT
1 ATATTTATTAAATAAATCATTT
1639586 ATAT
1 ATAT
1639590 AAAAATTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (22 bp):
ATATTTATTAAATAAATCATTT
Found at i:1639874 original size:21 final size:21
Alignment explanation
Indices: 1639850--1639900 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
1639840 ATTATTAATT
1639850 TTAATTTTAAAATTATAATAA
1 TTAATTTTAAAATTATAATAA
***
1639871 TTAATTTTATTGTTATAATAA
1 TTAATTTTAAAATTATAATAA
1639892 TTAATTTTA
1 TTAATTTTA
1639901 TTTTTATTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
TTAATTTTAAAATTATAATAA
Found at i:1639901 original size:21 final size:21
Alignment explanation
Indices: 1639862--1639912 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
1639852 AATTTTAAAA
1639862 TTATAATAATTAATTTTATTG
1 TTATAATAATTAATTTTATTG
*
1639883 TTATAATAATTAATTTTATTT
1 TTATAATAATTAATTTTATTG
1639904 TTATTAATA
1 TTA-TAATA
1639913 TTTTTAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 23 0.82
22 5 0.18
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (21 bp):
TTATAATAATTAATTTTATTG
Found at i:1640340 original size:28 final size:28
Alignment explanation
Indices: 1640287--1640340 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
1640277 AATAATTTTT
*
1640287 TTTTAAAAATTAATTTTATATATATTTA
1 TTTTAAAAATAAATTTTATATATATTTA
*
1640315 TTTTAAAAATAAAATTTT-TATTTATT
1 TTTTAAAAAT-AAATTTTATATATATT
1640341 AATAAATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 17 0.74
29 6 0.26
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (28 bp):
TTTTAAAAATAAATTTTATATATATTTA
Found at i:1642224 original size:9 final size:9
Alignment explanation
Indices: 1642209--1642243 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
1642199 ATTATTATTA
1642209 TTATTGTTG
1 TTATTGTTG
*
1642218 TTGTTGTTG
1 TTATTGTTG
*
1642227 TTATTATTG
1 TTATTGTTG
1642236 TTATTGTT
1 TTATTGTT
1642244 TATTTCTTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.11, C:0.00, G:0.20, T:0.69
Consensus pattern (9 bp):
TTATTGTTG
Found at i:1643155 original size:20 final size:18
Alignment explanation
Indices: 1643118--1643163 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 18
1643108 GGTTCAAGTA
*
1643118 AAATTTTTTTTTTTTTTT
1 AAATTTTTTTTTTATTTT
1643136 AAATTTATTTTTGTTATTTT
1 AAATTT-TTTTT-TTATTTT
1643156 AAATTTTT
1 AAATTTTT
1643164 ATCATTAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 6 0.24
19 7 0.28
20 12 0.48
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (18 bp):
AAATTTTTTTTTTATTTT
Found at i:1643439 original size:12 final size:12
Alignment explanation
Indices: 1643424--1643462 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1643414 AATTAAAAAT
*
1643424 AAAAAATAGTAA
1 AAAAAATAATAA
*
1643436 AAAAATTAATAA
1 AAAAAATAATAA
*
1643448 TAAAAATAATAA
1 AAAAAATAATAA
1643460 AAA
1 AAA
1643463 TTAATAAAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.21
Consensus pattern (12 bp):
AAAAAATAATAA
Found at i:1643444 original size:25 final size:24
Alignment explanation
Indices: 1643412--1643462 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
1643402 TAAATTTTTT
*
1643412 AAAATTAAAAATAAAAAATAGTAAA
1 AAAATTAAAAAT-AAAAATAATAAA
*
1643437 AAAATTAATAATAAAAATAATAAA
1 AAAATTAAAAATAAAAATAATAAA
1643461 AA
1 AA
1643463 TTAATAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 13 0.54
25 11 0.46
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (24 bp):
AAAATTAAAAATAAAAATAATAAA
Found at i:1643455 original size:9 final size:9
Alignment explanation
Indices: 1643443--1643473 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
1643433 TAAAAAAATT
1643443 AATAATAAA
1 AATAATAAA
1643452 AATAATAAA
1 AATAATAAA
1643461 AATTAATAAA
1 AA-TAATAAA
1643471 AAT
1 AAT
1643474 GTAAGAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (9 bp):
AATAATAAA
Found at i:1643467 original size:10 final size:10
Alignment explanation
Indices: 1643445--1643483 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
1643435 AAAAAATTAA
1643445 TAATAAAAA-
1 TAATAAAAAT
1643454 TAATAAAAAT
1 TAATAAAAAT
1643464 TAATAAAAAT
1 TAATAAAAAT
*
1643474 GTAAGAAAAA
1 -TAATAAAAA
1643484 AAAATTTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
9 9 0.33
10 10 0.37
11 8 0.30
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (10 bp):
TAATAAAAAT
Found at i:1643484 original size:22 final size:22
Alignment explanation
Indices: 1643412--1643469 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 22
1643402 TAAATTTTTT
*
1643412 AAAATTAAAAATAAAAAATAGTAAA
1 AAAATTAATAAT-AAAAATA--AAA
*
1643437 AAAATTAATAATAAAAATAATA
1 AAAATTAATAATAAAAATAAAA
1643459 AAAATTAATAA
1 AAAATTAATAA
1643470 AAATGTAAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
22 13 0.42
24 7 0.23
25 11 0.35
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (22 bp):
AAAATTAATAATAAAAATAAAA
Found at i:1648028 original size:18 final size:19
Alignment explanation
Indices: 1648005--1648040 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1647995 TCTGACCGAA
*
1648005 AAACTT-GTCTAAAAATTC
1 AAACTTCGTCGAAAAATTC
1648023 AAACTTCGTCGAAAAATT
1 AAACTTCGTCGAAAAATT
1648041 TCGTCGGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.44, C:0.17, G:0.08, T:0.31
Consensus pattern (19 bp):
AAACTTCGTCGAAAAATTC
Found at i:1648458 original size:13 final size:13
Alignment explanation
Indices: 1648442--1648491 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
1648432 AGAAATAGAT
1648442 AAATAATAATAAC
1 AAATAATAATAAC
1648455 AAATAATAA-AAGC
1 AAATAATAATAA-C
*
1648468 AGATAAATAATAA-
1 AAAT-AATAATAAC
*
1648481 AAATATTAATA
1 AAATAATAATA
1648492 GATAAAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
12 8 0.26
13 16 0.52
14 5 0.16
15 2 0.06
ACGTcount: A:0.68, C:0.04, G:0.04, T:0.24
Consensus pattern (13 bp):
AAATAATAATAAC
Found at i:1648459 original size:10 final size:9
Alignment explanation
Indices: 1648425--1648557 Score: 55
Period size: 9 Copynumber: 14.7 Consensus size: 9
1648415 ATAATTGGAT
1648425 AAATAA-AA
1 AAATAATAA
1648433 GAAATAGATAA
1 -AAATA-ATAA
1648444 ATAATAATAA
1 A-AATAATAA
1648454 CAAATAATAA
1 -AAATAATAA
**
1648464 AAGCAGAT--
1 AAATA-ATAA
1648472 AAATAATAA
1 AAATAATAA
*
1648481 AAATATTAA
1 AAATAATAA
*
1648490 TAGATAA-AA
1 -AAATAATAA
*
1648499 AAATAA-AT
1 AAATAATAA
* *
1648507 ATATATTAA
1 AAATAATAA
* *
1648516 TAAAT-AGAC
1 -AAATAATAA
1648525 AAATAATAA
1 AAATAATAA
1648534 AAATAA-AA
1 AAATAATAA
*
1648542 ATAAAAATAA
1 A-AATAATAA
1648552 AAATAA
1 AAATAA
1648558 AAGCCAATTG
Statistics
Matches: 91, Mismatches: 20, Indels: 26
0.66 0.15 0.19
Matches are distributed among these distances:
7 2 0.02
8 20 0.22
9 36 0.40
10 26 0.29
11 7 0.08
ACGTcount: A:0.71, C:0.02, G:0.05, T:0.23
Consensus pattern (9 bp):
AAATAATAA
Found at i:1648494 original size:23 final size:26
Alignment explanation
Indices: 1648468--1648517 Score: 70
Period size: 24 Copynumber: 2.0 Consensus size: 26
1648458 TAATAAAAGC
*
1648468 AGAT-AAATAATAAA-A-ATATTAAT
1 AGATAAAAAAATAAATATATATTAAT
1648491 AGATAAAAAAATAAATATATATTAAT
1 AGATAAAAAAATAAATATATATTAAT
1648517 A
1 A
1648518 AATAGACAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 4 0.17
24 9 0.39
25 1 0.04
26 9 0.39
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (26 bp):
AGATAAAAAAATAAATATATATTAAT
Found at i:1648528 original size:26 final size:24
Alignment explanation
Indices: 1648476--1648559 Score: 80
Period size: 24 Copynumber: 3.3 Consensus size: 24
1648466 GCAGATAAAT
*
1648476 AATAAAAATATTAATAGATAAAAA
1 AATAAAAATATTAATAAATAAAAA
1648500 AATAAATATATATTAATAAATAGACAAA
1 AATAAA-A-ATATTAATAAATA-A-AAA
**
1648528 TAATAAAAATAAAAATAAA-AATAAA
1 -AATAAAAATATTAATAAATAA-AAA
1648553 AATAAAA
1 AATAAAA
1648560 GCCAATTGGG
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
24 13 0.25
25 5 0.10
26 13 0.25
27 10 0.20
28 4 0.08
29 6 0.12
ACGTcount: A:0.73, C:0.01, G:0.02, T:0.24
Consensus pattern (24 bp):
AATAAAAATATTAATAAATAAAAA
Found at i:1648540 original size:6 final size:6
Alignment explanation
Indices: 1648529--1648559 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
1648519 ATAGACAAAT
1648529 AATAAA AATAAA AATAAA AATAAA AATAAA A
1 AATAAA AATAAA AATAAA AATAAA AATAAA A
1648560 GCCAATTGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AATAAA
Found at i:1648912 original size:41 final size:41
Alignment explanation
Indices: 1648777--1649023 Score: 284
Period size: 41 Copynumber: 6.0 Consensus size: 41
1648767 TTTGATCAAA
* **
1648777 GCTCCTCTAAGT-AGAGGCTCTACGACTTTGAAAAAATAAACAAA
1 GCTCCTCTAA-TCAGAGGCTCAACGACTTTG-AAAAAT-AA-ATG
* * * *
1648821 GCTCCTCTAAACAGAGGCTCTATGACCTTG-AAAATAAATG
1 GCTCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAATG
1648861 GCTTCC-CTAATCAGAGGCTCAACGACTTTGAAAAATAAATG
1 GC-TCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAATG
* * *
1648902 GCTCCTCTAATCAGAGGCTAAACAACTTTGAAAAACAAATG
1 GCTCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAATG
* * *
1648943 GCTCCTCTAATAAGAGGCTTAACGACTTTGGAAAATAAATG
1 GCTCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAATG
* * *
1648984 GCTCCTCTAACCAGAGGTTCAACAACTTTGAAAAATAAAT
1 GCTCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAAT
1649024 AAATTCTCTA
Statistics
Matches: 176, Mismatches: 23, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
40 26 0.15
41 119 0.68
42 5 0.03
44 26 0.15
ACGTcount: A:0.38, C:0.21, G:0.16, T:0.24
Consensus pattern (41 bp):
GCTCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAATG
Found at i:1649033 original size:82 final size:82
Alignment explanation
Indices: 1648867--1649081 Score: 238
Period size: 82 Copynumber: 2.6 Consensus size: 82
1648857 AATGGCTTCC
* *
1648867 CTAATCAGAGGCTCAACGACTTTGAAAAATAAATGGCTCCTCTAATCAGAGGCTAAACAACTTTG
1 CTAATAAGAGGCTCAACGACTTTGAAAAATAAATGGCTCCTCTAACCAGAGGCTAAACAACTTTG
***
1648932 AAAAACAAATGGCTCCT
66 AAAAACAAATAAATCCT
* * * *
1648949 CTAATAAGAGGCTTAACGACTTTGGAAAATAAATGGCTCCTCTAACCAGAGGTTCAACAACTTTG
1 CTAATAAGAGGCTCAACGACTTTGAAAAATAAATGGCTCCTCTAACCAGAGGCTAAACAACTTTG
* *
1649014 AAAAATAAATAAATTCT
66 AAAAACAAATAAATCCT
* * * * * * *
1649031 CTAA-ACAAAAGCACCATGAC-TTCAAAAATAAAT-GCTCCTCTAAACAGAGGC
1 CTAATA-AGAGGCTCAACGACTTTGAAAAATAAATGGCTCCTCTAACCAGAGGC
1649082 ACCACAAATT
Statistics
Matches: 111, Mismatches: 21, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
80 16 0.14
81 12 0.11
82 83 0.75
ACGTcount: A:0.41, C:0.21, G:0.14, T:0.23
Consensus pattern (82 bp):
CTAATAAGAGGCTCAACGACTTTGAAAAATAAATGGCTCCTCTAACCAGAGGCTAAACAACTTTG
AAAAACAAATAAATCCT
Found at i:1649463 original size:43 final size:42
Alignment explanation
Indices: 1649409--1649490 Score: 130
Period size: 43 Copynumber: 1.9 Consensus size: 42
1649399 TTTGGCAAAC
*
1649409 TTGGAATTCATATCCAAAAAT-CTAAAGCTTTTCATTTGAATT
1 TTGGAATTCATATCCAAAAATGC-AAAGCTTCTCATTTGAATT
1649451 TTGGAGATTCATATCCAAAAATGCAAAGCTTCTCATTTGA
1 TTGGA-ATTCATATCCAAAAATGCAAAGCTTCTCATTTGA
1649491 GTTCAAAGGC
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
42 5 0.14
43 31 0.84
44 1 0.03
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (42 bp):
TTGGAATTCATATCCAAAAATGCAAAGCTTCTCATTTGAATT
Found at i:1650927 original size:24 final size:24
Alignment explanation
Indices: 1650900--1650949 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
1650890 CTTTTTTTTC
1650900 TTTTTTTTTCTTCACCTTTCA-CCA
1 TTTTTTTTTC-TCACCTTTCATCCA
*
1650924 TTTTTTTTTCTCATCTTTCATCCA
1 TTTTTTTTTCTCACCTTTCATCCA
1650948 TT
1 TT
1650950 ATTGATATCT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 9 0.38
24 15 0.62
ACGTcount: A:0.12, C:0.26, G:0.00, T:0.62
Consensus pattern (24 bp):
TTTTTTTTTCTCACCTTTCATCCA
Found at i:1657534 original size:25 final size:25
Alignment explanation
Indices: 1657501--1657552 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
1657491 AAATCTAGAC
1657501 AAAATTTTCACCT-AAGAATTTTATA
1 AAAATTTTCACCTGAA-AATTTTATA
* *
1657526 AAAATTTTCATCTGAAATTTTTATA
1 AAAATTTTCACCTGAAAATTTTATA
1657551 AA
1 AA
1657553 TTCCATCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 22 0.92
26 2 0.08
ACGTcount: A:0.44, C:0.10, G:0.04, T:0.42
Consensus pattern (25 bp):
AAAATTTTCACCTGAAAATTTTATA
Found at i:1658524 original size:22 final size:24
Alignment explanation
Indices: 1658499--1658554 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 24
1658489 AAAATAAAAG
1658499 TAGATAAATAATAAA-ATAT-TAA
1 TAGATAAATAATAAATATATATAA
* *
1658521 TAGATAAAAAAATAAATATATATAC
1 TAGAT-AAATAATAAATATATATAA
1658546 TA-ATAAATA
1 TAGATAAATA
1658555 GACAAATAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 5 0.18
23 13 0.46
24 6 0.21
25 4 0.14
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (24 bp):
TAGATAAATAATAAATATATATAA
Found at i:1660113 original size:20 final size:19
Alignment explanation
Indices: 1660084--1660130 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
1660074 GGTTCAAGTA
* *
1660084 AAATTTTTTTTTTTTTTTT
1 AAATTTTTTTTGTTATTTT
1660103 AAATTTATTTTTGTTATTTT
1 AAATTT-TTTTTGTTATTTT
1660123 AAATTTTT
1 AAATTTTT
1660131 ATCATTAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.74
Consensus pattern (19 bp):
AAATTTTTTTTGTTATTTT
Found at i:1660406 original size:12 final size:12
Alignment explanation
Indices: 1660391--1660429 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1660381 AATTAAAAAT
*
1660391 AAAAAATAGTAA
1 AAAAAATAATAA
*
1660403 AAAAATTAATAA
1 AAAAAATAATAA
*
1660415 TAAAAATAATAA
1 AAAAAATAATAA
1660427 AAA
1 AAA
1660430 TTAATAAAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.21
Consensus pattern (12 bp):
AAAAAATAATAA
Found at i:1660411 original size:25 final size:24
Alignment explanation
Indices: 1660379--1660429 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
1660369 TAAATTTTTT
*
1660379 AAAATTAAAAATAAAAAATAGTAAA
1 AAAATTAAAAAT-AAAAATAATAAA
*
1660404 AAAATTAATAATAAAAATAATAAA
1 AAAATTAAAAATAAAAATAATAAA
1660428 AA
1 AA
1660430 TTAATAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 13 0.54
25 11 0.46
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (24 bp):
AAAATTAAAAATAAAAATAATAAA
Found at i:1660422 original size:9 final size:9
Alignment explanation
Indices: 1660410--1660440 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
1660400 TAAAAAAATT
1660410 AATAATAAA
1 AATAATAAA
1660419 AATAATAAA
1 AATAATAAA
1660428 AATTAATAAA
1 AA-TAATAAA
1660438 AAT
1 AAT
1660441 GTAAGAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (9 bp):
AATAATAAA
Found at i:1660434 original size:10 final size:10
Alignment explanation
Indices: 1660412--1660450 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
1660402 AAAAAATTAA
1660412 TAATAAAAA-
1 TAATAAAAAT
1660421 TAATAAAAAT
1 TAATAAAAAT
1660431 TAATAAAAAT
1 TAATAAAAAT
*
1660441 GTAAGAAAAA
1 -TAATAAAAA
1660451 AAATTTTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
9 9 0.33
10 10 0.37
11 8 0.30
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (10 bp):
TAATAAAAAT
Found at i:1660451 original size:22 final size:22
Alignment explanation
Indices: 1660379--1660436 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 22
1660369 TAAATTTTTT
*
1660379 AAAATTAAAAATAAAAAATAGTAAA
1 AAAATTAATAAT-AAAAATA--AAA
*
1660404 AAAATTAATAATAAAAATAATA
1 AAAATTAATAATAAAAATAAAA
1660426 AAAATTAATAA
1 AAAATTAATAA
1660437 AAATGTAAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
22 13 0.42
24 7 0.23
25 11 0.35
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (22 bp):
AAAATTAATAATAAAAATAAAA
Found at i:1660453 original size:33 final size:31
Alignment explanation
Indices: 1660385--1660454 Score: 79
Period size: 31 Copynumber: 2.2 Consensus size: 31
1660375 TTTTAAAATT
* *
1660385 AAAAATAAAAAATAGTAAAAAAATTAATAAT
1 AAAAATAAAAAATAGTAAAAAAATTAAGAAA
*
1660416 AAAAATAATAAAA-ATTAATAAAAATGTAAGAAA
1 AAAAATAA-AAAATAGTAA-AAAAAT-TAAGAAA
1660449 AAAAAT
1 AAAAAT
1660455 TTTTATCCGA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 12 0.36
32 10 0.30
33 11 0.33
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.21
Consensus pattern (31 bp):
AAAAATAAAAAATAGTAAAAAAATTAAGAAA
Found at i:1665624 original size:25 final size:24
Alignment explanation
Indices: 1665577--1665641 Score: 58
Period size: 26 Copynumber: 2.6 Consensus size: 24
1665567 CAAATTTAGA
* * *
1665577 AAAAATTTCTCATCTAGAGATTTTTT
1 AAAAATTTATCAT-TAGA-AATTTCT
*
1665603 AAAAATTTATCATTTGAAATTTCT
1 AAAAATTTATCATTAGAAATTTCT
*
1665627 AAGAATCTTATCATT
1 AAAAAT-TTATCATT
1665642 GGGTAATTTG
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
24 10 0.30
25 11 0.33
26 12 0.36
ACGTcount: A:0.38, C:0.11, G:0.06, T:0.45
Consensus pattern (24 bp):
AAAAATTTATCATTAGAAATTTCT
Found at i:1665704 original size:17 final size:17
Alignment explanation
Indices: 1665668--1665711 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
1665658 ATTCCAAAAA
*
1665668 TTTTATGTTTTTATGCT
1 TTTTATGTTTTTATACT
* *
1665685 TTTTATGTTTTTTTATT
1 TTTTATGTTTTTATACT
*
1665702 TTTTTTGTTT
1 TTTTATGTTT
1665712 GAAAATATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.09, C:0.02, G:0.09, T:0.80
Consensus pattern (17 bp):
TTTTATGTTTTTATACT
Found at i:1666331 original size:18 final size:19
Alignment explanation
Indices: 1666308--1666343 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1666298 TCTGACTGAA
*
1666308 AAACTT-GTCTAAAAATTC
1 AAACTTCGTCGAAAAATTC
1666326 AAACTTCGTCGAAAAATT
1 AAACTTCGTCGAAAAATT
1666344 TCGTCAGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.44, C:0.17, G:0.08, T:0.31
Consensus pattern (19 bp):
AAACTTCGTCGAAAAATTC
Found at i:1666749 original size:8 final size:7
Alignment explanation
Indices: 1666738--1666869 Score: 55
Period size: 6 Copynumber: 18.9 Consensus size: 7
1666728 TAAATAAAAG
1666738 AAATAGAT
1 AAATA-AT
1666746 AAATAAT
1 AAATAAT
* *
1666753 -AATTAC
1 AAATAAT
1666759 AAATAAT
1 AAATAAT
*
1666766 AAAAGCAGAT
1 -AAA-TA-AT
1666776 AAATAAT
1 AAATAAT
1666783 AAA-AAT
1 AAATAAT
*
1666789 -ATTAAT
1 AAATAAT
* *
1666795 AGATAAAA
1 AAAT-AAT
1666803 AAATAA-
1 AAATAAT
1666809 AAATATAT
1 AAATA-AT
*
1666817 ATATTAAT
1 A-AATAAT
*
1666825 AAATAGAC
1 AAATA-AT
1666833 AAATAAT
1 AAATAAT
1666840 AAA-AAT
1 AAATAAT
*
1666846 AAA-AAA
1 AAATAAT
1666852 AAATAA-
1 AAATAAT
1666858 AAATAA-
1 AAATAAT
1666864 AAATAA
1 AAATAA
1666870 AAGCCAATTG
Statistics
Matches: 96, Mismatches: 16, Indels: 26
0.70 0.12 0.19
Matches are distributed among these distances:
5 1 0.01
6 38 0.40
7 24 0.25
8 24 0.25
9 7 0.07
10 2 0.02
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.23
Consensus pattern (7 bp):
AAATAAT
Found at i:1666823 original size:30 final size:33
Alignment explanation
Indices: 1666787--1666846 Score: 90
Period size: 30 Copynumber: 1.9 Consensus size: 33
1666777 AATAATAAAA
*
1666787 ATATTAATAGATA-A-AAA-AATAAAAATATAT
1 ATATTAATAAATAGACAAATAATAAAAATATAT
1666817 ATATTAATAAATAGACAAATAATAAAAATA
1 ATATTAATAAATAGACAAATAATAAAAATA
1666847 AAAAAAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 12 0.46
31 1 0.04
32 3 0.12
33 10 0.38
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (33 bp):
ATATTAATAAATAGACAAATAATAAAAATATAT
Found at i:1666858 original size:16 final size:17
Alignment explanation
Indices: 1666837--1666871 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
1666827 ATAGACAAAT
1666837 AATAAAAATAAAAA-AA
1 AATAAAAATAAAAATAA
1666853 AATAAAAATAAAAATAA
1 AATAAAAATAAAAATAA
1666870 AA
1 AA
1666872 GCCAATTGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (17 bp):
AATAAAAATAAAAATAA
Found at i:1667224 original size:41 final size:41
Alignment explanation
Indices: 1667088--1667340 Score: 208
Period size: 41 Copynumber: 6.2 Consensus size: 41
1667078 TTTTGATCAA
** * *
1667088 AGCTCCTCTAAGTAGAGGCTCTACGACTTTGAAAAAATAAACAA
1 AGCTCCTCTAAACAGAGGCTCAACGACTTTG-AAAAAT-AA-AT
* * *
1667132 AGCTCCTCTAAACAGAGGCTCTATGACCTTG-AAAATAAAT
1 AGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAAT
* *
1667172 GGCTTCC-CTAATCAGAGGCTCAACGACTTTGAAAAATAAAT
1 AGC-TCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAAT
* * * *
1667213 GGCTCCTCTAATCAGAGGTTCAACAACTTTGAAAAATAAAT
1 AGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAAT
** * * * * * *
1667254 AAATTCTCTAAACAGAAGCACCATGAC-TTCAAAAATAAAT
1 AGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAAT
* * * *
1667294 -GCTCCTCTAAACAGAGGCACCACAACTTTGAAAAGTAAAT
1 AGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAAT
*
1667334 TGCTCCT
1 AGCTCCT
1667341 TAACAATCAT
Statistics
Matches: 172, Mismatches: 32, Indels: 13
0.79 0.15 0.06
Matches are distributed among these distances:
39 20 0.12
40 49 0.28
41 71 0.41
42 5 0.03
44 27 0.16
ACGTcount: A:0.40, C:0.22, G:0.14, T:0.24
Consensus pattern (41 bp):
AGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAAT
Found at i:1667356 original size:121 final size:124
Alignment explanation
Indices: 1667113--1667340 Score: 277
Period size: 121 Copynumber: 1.9 Consensus size: 124
1667103 AGGCTCTACG
* * * *
1667113 ACTTTGAAAAAATAAACAAAGCTCCTCTAAACAGAGGCTCTATGACCTTGAAAATAAATGGCTTC
1 ACTTTGAAAAAATAAACAAA-CTCCTCTAAACAGAAGCACCATGACCTTAAAAATAAATGGCTTC
* * * *
1667178 CCTAATCAGAGGCTCAACGACTTTGAAAAATAAATGGCTCCTCTAATCAGAGGTTCAACA
65 CCTAAACAGAGGCACAACAACTTTGAAAAATAAATGGCTCCTCTAATCACAGGTTCAACA
* *
1667238 ACTTTG-AAAAATAAATAAA-TTCTCTAAACAGAAGCACCATGA-CTTCAAAAATAAAT-GC-TC
1 ACTTTGAAAAAATAAACAAACTCCTCTAAACAGAAGCACCATGACCTT-AAAAATAAATGGCTTC
* * *
1667298 CTCTAAACAGAGGCACCACAACTTTGAAAAGTAAATTGCTCCT
65 C-CTAAACAGAGGCACAACAACTTTGAAAAATAAATGGCTCCT
1667341 TAACAATCAT
Statistics
Matches: 89, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
120 3 0.03
121 40 0.45
122 28 0.31
124 12 0.13
125 6 0.07
ACGTcount: A:0.41, C:0.21, G:0.13, T:0.24
Consensus pattern (124 bp):
ACTTTGAAAAAATAAACAAACTCCTCTAAACAGAAGCACCATGACCTTAAAAATAAATGGCTTCC
CTAAACAGAGGCACAACAACTTTGAAAAATAAATGGCTCCTCTAATCACAGGTTCAACA
Found at i:1667693 original size:43 final size:42
Alignment explanation
Indices: 1667639--1667720 Score: 130
Period size: 43 Copynumber: 1.9 Consensus size: 42
1667629 TTTGGCAAAC
*
1667639 TTGGAATTCATATCCAAAAAT-CTAAAGCTTTTCATTTGAATT
1 TTGGAATTCATATCCAAAAATGC-AAAGCTTCTCATTTGAATT
1667681 TTGGAGATTCATATCCAAAAATGCAAAGCTTCTCATTTGA
1 TTGGA-ATTCATATCCAAAAATGCAAAGCTTCTCATTTGA
1667721 GTTCAAAGGC
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
42 5 0.14
43 31 0.84
44 1 0.03
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (42 bp):
TTGGAATTCATATCCAAAAATGCAAAGCTTCTCATTTGAATT
Found at i:1669157 original size:27 final size:28
Alignment explanation
Indices: 1669102--1669158 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
1669092 TCATTTAATC
*
1669102 TTTTTTTTCTTTTTTTTATTTTCCCCCT
1 TTTTTTTTCTTTTTTTTATTTTCCACCT
1669130 TTTTTTTTCTTTTTTTT-TTCTT-CACCT
1 TTTTTTTTCTTTTTTTTATT-TTCCACCT
1669157 TT
1 TT
1669159 CACCATTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 8 0.30
28 19 0.70
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (28 bp):
TTTTTTTTCTTTTTTTTATTTTCCACCT
Found at i:1669170 original size:22 final size:23
Alignment explanation
Indices: 1669141--1669188 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
1669131 TTTTTTTCTT
1669141 TTTTTTTTCTTCACCTTTCA-CCA
1 TTTTTTTTC-TCACCTTTCATCCA
*
1669164 TTTTTTTTCTCATCTTTCATCCA
1 TTTTTTTTCTCACCTTTCATCCA
1669187 TT
1 TT
1669189 ATTGATATCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.12, C:0.27, G:0.00, T:0.60
Consensus pattern (23 bp):
TTTTTTTTCTCACCTTTCATCCA
Found at i:1676694 original size:17 final size:16
Alignment explanation
Indices: 1676672--1676715 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
1676662 ATATTAATAG
*
1676672 ATAAAAAAATTGGATAA
1 ATAAAAAAA-TAGATAA
1676689 ATAAAAGAAATAGATAA
1 ATAAAA-AAATAGATAA
1676706 ATAATAAAAA
1 ATAA-AAAAA
1676716 AATAAAAGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 19 0.79
18 5 0.21
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.20
Consensus pattern (16 bp):
ATAAAAAAATAGATAA
Found at i:1676694 original size:42 final size:42
Alignment explanation
Indices: 1676645--1676762 Score: 113
Period size: 38 Copynumber: 2.9 Consensus size: 42
1676635 AAAATAATTA
***
1676645 AAATAAAAAAGATAAATATATTAATAGATAAAAAAATTGGA-T
1 AAAT-AAAAAGATAAATATATTAATAGATAAAAAAATAAAAGT
* *
1676687 AAAT-AAAAG--AAATAGATAAATA-ATAAAAAAATAAAAGT
1 AAATAAAAAGATAAATATATTAATAGATAAAAAAATAAAAGT
* * *
1676725 AGATAAATA-ATAAAAATATTAATAGATAAAAAAATAAA
1 AAATAAAAAGATAAATATATTAATAGATAAAAAAATAAA
1676763 TATATATACT
Statistics
Matches: 61, Mismatches: 10, Indels: 11
0.74 0.12 0.13
Matches are distributed among these distances:
37 11 0.18
38 15 0.25
39 3 0.05
40 15 0.25
41 13 0.21
42 4 0.07
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (42 bp):
AAATAAAAAGATAAATATATTAATAGATAAAAAAATAAAAGT
Found at i:1676778 original size:24 final size:24
Alignment explanation
Indices: 1676697--1676767 Score: 67
Period size: 24 Copynumber: 3.0 Consensus size: 24
1676687 AAATAAAAGA
*
1676697 AATAGATAAATAATAA-AAAAATA-A
1 AATAGATAAA-AA-AATAAAAATATT
*
1676721 AAGTAGAT-AAATAATAAAAATATT
1 AA-TAGATAAAAAAATAAAAATATT
*
1676745 AATAGATAAAAAAATAAATATAT
1 AATAGATAAAAAAATAAAAATAT
1676768 ATACTAATAA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
22 2 0.05
23 13 0.33
24 19 0.49
25 5 0.13
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (24 bp):
AATAGATAAAAAAATAAAAATATT
Found at i:1676795 original size:78 final size:77
Alignment explanation
Indices: 1676656--1676800 Score: 186
Period size: 78 Copynumber: 1.9 Consensus size: 77
1676646 AATAAAAAAG
* ** *
1676656 ATAAATATATTAATAGATAAAAAAATTGGATAAATAAAAGAAATAGATAAATAATAAAAAAATAA
1 ATAAAAATATTAATAGATAAAAAAATTAAATAAATAAAAGAAATAGACAAATAAT-AAAAAATAA
1676721 AAGTAGATAAATA
65 AAGTAGATAAATA
* *
1676734 ATAAAAATATTAATAGATAAAAAAA-TAAATATATATACTAATAAATAGACAAATAAT-AAAAAT
1 ATAAAAATATTAATAGATAAAAAAATTAAATA-A-ATA-AAAGAAATAGACAAATAATAAAAAAT
1676797 AAAA
63 AAAA
1676801 ATAAAAGCCA
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
77 4 0.07
78 35 0.60
79 3 0.05
80 16 0.28
ACGTcount: A:0.68, C:0.01, G:0.06, T:0.25
Consensus pattern (77 bp):
ATAAAAATATTAATAGATAAAAAAATTAAATAAATAAAAGAAATAGACAAATAATAAAAAATAAA
AGTAGATAAATA
Found at i:1681696 original size:145 final size:145
Alignment explanation
Indices: 1681538--1681942 Score: 433
Period size: 145 Copynumber: 2.8 Consensus size: 145
1681528 TTGATTAGAG
* * * ** *
1681538 AAAGTATGAAATTACCAAAATACTCCTATAATGATATTTTTGTAATTTAATCTTTTTGAGCTCAA
1 AAAGTGTGAAATTACCAAAATACTCCTATAAAGGTATTTTCATAATTTAA-CTTCTTGAGCTCAA
* * * * *
1681603 ATTTTCATAAAACTTTTCATATCTTAACTTCATAATATTTCATGATTTTTGA-TGCATTCAAAAT
65 ATTTTCATGAAACTTTTTAAATCTTAATTTCATAATATTTCATGATTTTTAAGTGCATTCAAAAT
* * * *
1681667 CACAATCGTATCTCGA
130 CACAATAGTACCCCAA
* * *
1681683 GAAGTGTGAAATTACCAAAATA-TCTTTATAAAGGTATTTTCATAATTTAACATTCTCGAGC-CT
1 AAAGTGTGAAATTACCAAAATACTC-CTATAAAGGTATTTTCATAATTTAAC-TTCTTGAGCTC-
** * * **
1681746 GGATTTTCATGAAACTTTTTAGATCTTAATTTCATAATATTTCATG-GTTTTAAGTGCATTTGAA
63 AAATTTTCATGAAACTTTTTAAATCTTAATTTCATAATATTTCATGATTTTTAAGTGCATTCAAA
* * *
1681810 GTCATAGTAGTACCCCAA
128 ATCACAATAGTACCCCAA
* * *
1681828 AAAGTGTGAAATTATCAAAATAC-CCTTATAAAGGTATTTTCATAATTTGACCTTCCTGAGCTCA
1 AAAGTGTGAAATTACCAAAATACTCC-TATAAAGGTATTTTCATAATTT-AACTTCTTGAGCTCA
* *
1681892 AATTTTCATGAAACTTTTTAAATCTCAATTTTATAATATTTCATGATTTTT
64 AATTTTCATGAAACTTTTTAAATCTTAATTTCATAATATTTCATGATTTTT
1681943 TGTGTTTTAA
Statistics
Matches: 213, Mismatches: 38, Indels: 17
0.79 0.14 0.06
Matches are distributed among these distances:
144 9 0.04
145 197 0.92
146 7 0.03
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (145 bp):
AAAGTGTGAAATTACCAAAATACTCCTATAAAGGTATTTTCATAATTTAACTTCTTGAGCTCAAA
TTTTCATGAAACTTTTTAAATCTTAATTTCATAATATTTCATGATTTTTAAGTGCATTCAAAATC
ACAATAGTACCCCAA
Found at i:1682474 original size:24 final size:24
Alignment explanation
Indices: 1682447--1682529 Score: 78
Period size: 24 Copynumber: 3.3 Consensus size: 24
1682437 CTGCTGAAGG
*
1682447 AAGAAAAGAAAAGAAGTTGCCAAA
1 AAGAAAAGAAAAGAAGTTGCAAAA
*
1682471 AAGAAAAGAAGAGAAAGCTGTTG-AAAA
1 AAGAAAAGAAAAG-AA---GTTGCAAAA
* *
1682498 AAGAAAAGAAAATGAAGTTGCTAGA
1 AAGAAAAGAAAA-GAAGTTGCAAAA
1682523 AAGAAAA
1 AAGAAAA
1682530 AGAAGAACAA
Statistics
Matches: 48, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
24 16 0.33
25 11 0.23
27 16 0.33
28 5 0.10
ACGTcount: A:0.61, C:0.05, G:0.23, T:0.11
Consensus pattern (24 bp):
AAGAAAAGAAAAGAAGTTGCAAAA
Found at i:1682502 original size:51 final size:53
Alignment explanation
Indices: 1682429--1682549 Score: 149
Period size: 51 Copynumber: 2.3 Consensus size: 53
1682419 AAAGGACTGG
* * **
1682429 AGAGGAAGCTGCTGAAGGAAGAAAAGAAAA-GAAGTTGCCAAAAAG-AAAAGA
1 AGAGAAAGCTGTTGAAAAAAGAAAAGAAAATGAAGTTGCCAAAAAGAAAAAGA
* *
1682480 AGAGAAAGCTGTTGAAAAAAGAAAAGAAAATGAAGTTGCTAGAAAGAAAAAGA
1 AGAGAAAGCTGTTGAAAAAAGAAAAGAAAATGAAGTTGCCAAAAAGAAAAAGA
*
1682533 AGA-ACAAGCTGTCGAAA
1 AGAGA-AAGCTGTTGAAA
1682550 GTGGAAGAAA
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
51 26 0.43
52 14 0.23
53 20 0.33
ACGTcount: A:0.55, C:0.07, G:0.26, T:0.11
Consensus pattern (53 bp):
AGAGAAAGCTGTTGAAAAAAGAAAAGAAAATGAAGTTGCCAAAAAGAAAAAGA
Found at i:1682544 original size:53 final size:51
Alignment explanation
Indices: 1682447--1682549 Score: 145
Period size: 53 Copynumber: 2.0 Consensus size: 51
1682437 CTGCTGAAGG
*
1682447 AAGAAAAGAAAAGAAGTTGCCAAAAAGAAAAGAAGAGAAAGCTGTTGAAAA
1 AAGAAAAGAAAAGAAGTTGCCAAAAAGAAAAGAAGAGAAAGCTGTCGAAAA
* *
1682498 AAGAAAAGAAAATGAAGTTGCTAGAAAGAAAAAGAAGA-ACAAGCTGTCGAAA
1 AAGAAAAGAAAA-GAAGTTGCCAAAAAG-AAAAGAAGAGA-AAGCTGTCGAAA
1682550 GTGGAAGAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
51 12 0.26
52 14 0.30
53 20 0.43
ACGTcount: A:0.59, C:0.07, G:0.23, T:0.11
Consensus pattern (51 bp):
AAGAAAAGAAAAGAAGTTGCCAAAAAGAAAAGAAGAGAAAGCTGTCGAAAA
Found at i:1695350 original size:3 final size:3
Alignment explanation
Indices: 1695342--1695379 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
1695332 TTTTTGCATG
1695342 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1695380 ATTTTTACAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1696088 original size:44 final size:44
Alignment explanation
Indices: 1696034--1696121 Score: 124
Period size: 44 Copynumber: 2.0 Consensus size: 44
1696024 TTTGTAATTA
* *
1696034 TTTATGATTTTTCATGTGCACT-ATCTCTTTTGTTTATTTTGTAG
1 TTTATGATTTTTCATGTGCACTAATCT-ATATGTTTATTTTGTAG
* *
1696078 TTTATGATTTTTTATGTGTACTAATCTATATGTTTATTTTGTAG
1 TTTATGATTTTTCATGTGCACTAATCTATATGTTTATTTTGTAG
1696122 ATTTTAATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 35 0.90
45 4 0.10
ACGTcount: A:0.19, C:0.08, G:0.14, T:0.59
Consensus pattern (44 bp):
TTTATGATTTTTCATGTGCACTAATCTATATGTTTATTTTGTAG
Found at i:1696887 original size:14 final size:14
Alignment explanation
Indices: 1696859--1696895 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
1696849 TTGTTCTTAC
*
1696859 TATATA-TTGCATA
1 TATATATTTACATA
1696872 TATATATTTACATA
1 TATATATTTACATA
1696886 TATATATTTA
1 TATATATTTA
1696896 TCTATGTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 6 0.27
14 16 0.73
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (14 bp):
TATATATTTACATA
Found at i:1697824 original size:14 final size:16
Alignment explanation
Indices: 1697791--1697823 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1697781 TTGGCATTTT
1697791 AAAGAGAAAAAGGGAA
1 AAAGAGAAAAAGGGAA
*
1697807 AAAGA-AAAAAGTGAA
1 AAAGAGAAAAAGGGAA
1697822 AA
1 AA
1697824 GTAATTAGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.73, C:0.00, G:0.24, T:0.03
Consensus pattern (16 bp):
AAAGAGAAAAAGGGAA
Found at i:1698937 original size:21 final size:21
Alignment explanation
Indices: 1698913--1698962 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
1698903 CCACTTTGCC
* *
1698913 TAGTTTTTTTTTTCTTTTATT
1 TAGTTTTTTATTTCATTTATT
* *
1698934 TAGTCTTTTATTTCATTTGTT
1 TAGTTTTTTATTTCATTTATT
*
1698955 TTGTTTTT
1 TAGTTTTT
1698963 ATTATTTTCT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.10, C:0.06, G:0.08, T:0.76
Consensus pattern (21 bp):
TAGTTTTTTATTTCATTTATT
Found at i:1699163 original size:33 final size:34
Alignment explanation
Indices: 1699142--1699332 Score: 112
Period size: 38 Copynumber: 5.1 Consensus size: 34
1699132 TTGCTTGATG
*
1699142 TTTACTTGTATGATTTAATATTATTGCATGATTA
1 TTTACTTGCATGATTTAATATTATTGCATGATTA
** *
1699176 TTTGTTTGCATGATTTAATATTATCGCATGATTATTTA
1 TTTACTTGCATGATTTAATATTATTGCATG---A-TTA
* **
1699214 TTTATTTATATGATTTAATATTATTGCATGATTTAA
1 TTTACTTGCATGATTTAATATTATTGCATGA-TT-A
* * *
1699250 TATATTTGCATGATTATTAATATGTTATTTGCATCAGTTTAA
1 TTTACTTGCATGA-T-TTAATA--TTA-TTGCAT--GATT-A
* *
1699292 TTTAATTGCATGATTTATTATATAATTTTGCATGATTA
1 TTTACTTGCATGATTTA--ATAT--TATTGCATGATTA
1699330 TTT
1 TTT
1699333 TTGGGTGATT
Statistics
Matches: 125, Mismatches: 16, Indels: 28
0.74 0.09 0.17
Matches are distributed among these distances:
34 26 0.21
35 4 0.03
36 11 0.09
37 2 0.02
38 39 0.31
39 3 0.02
40 7 0.06
41 13 0.10
42 19 0.15
43 1 0.01
ACGTcount: A:0.30, C:0.06, G:0.11, T:0.53
Consensus pattern (34 bp):
TTTACTTGCATGATTTAATATTATTGCATGATTA
Found at i:1699174 original size:18 final size:18
Alignment explanation
Indices: 1699151--1699308 Score: 112
Period size: 18 Copynumber: 8.4 Consensus size: 18
1699141 GTTTACTTGT
1699151 ATGATTTAATATTATTGC
1 ATGATTTAATATTATTGC
*
1699169 ATGA-TT-AT-TTGTTTGC
1 ATGATTTAATATT-ATTGC
*
1699185 ATGATTTAATATTATCGC
1 ATGATTTAATATTATTGC
* **
1699203 ATGA-TTATTTATTTATTTAT
1 ATGATTTA-ATA-TTA-TTGC
1699223 ATGATTTAATATTATTGC
1 ATGATTTAATATTATTGC
1699241 ATGATTTAATA-TATTTGC
1 ATGATTTAATATTA-TTGC
1699259 ATGATTATTAATATGTTATTTGC
1 ATGA-T-TTAATA--TTA-TTGC
*
1699282 ATCAGTTTAAT-TTAATTGC
1 ATGA-TTTAATATT-ATTGC
1699301 ATGATTTA
1 ATGATTTA
1699309 TTATATAATT
Statistics
Matches: 112, Mismatches: 13, Indels: 30
0.72 0.08 0.19
Matches are distributed among these distances:
15 2 0.02
16 10 0.09
17 9 0.08
18 40 0.36
19 18 0.16
20 14 0.12
21 3 0.03
22 5 0.04
23 11 0.10
ACGTcount: A:0.31, C:0.06, G:0.11, T:0.52
Consensus pattern (18 bp):
ATGATTTAATATTATTGC
Found at i:1699182 original size:38 final size:37
Alignment explanation
Indices: 1699140--1699246 Score: 139
Period size: 34 Copynumber: 2.9 Consensus size: 37
1699130 TTTTGCTTGA
1699140 TGTTTACTTGTATGATTTAATATTATTGCATGATTATT
1 TGTTTA-TTGTATGATTTAATATTATTGCATGATTATT
* *
1699178 TG--T-TTGCATGATTTAATATTATCGCATGATTATT
1 TGTTTATTGTATGATTTAATATTATTGCATGATTATT
* *
1699212 TATTTATTTATATGATTTAATATTATTGCATGATT
1 TGTTTA-TTGTATGATTTAATATTATTGCATGATT
1699247 TAATATATTT
Statistics
Matches: 59, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
34 30 0.51
36 2 0.03
38 27 0.46
ACGTcount: A:0.28, C:0.06, G:0.12, T:0.54
Consensus pattern (37 bp):
TGTTTATTGTATGATTTAATATTATTGCATGATTATT
Found at i:1699242 original size:56 final size:59
Alignment explanation
Indices: 1699181--1699314 Score: 161
Period size: 56 Copynumber: 2.3 Consensus size: 59
1699171 GATTATTTGT
* *
1699181 TTGCATGATTTAATAT-TATCGCATGATTATT-TAT-TTATTTATATGA-TTTAATATT-A
1 TTGCATGATTTAATATAT-TCGCATGATTATTATATGTTATTTACATCAGTTTAAT-TTAA
* *
1699237 TTGCATGATTTAATATATTTGCATGATTATTAATATGTTATTTGCATCAGTTTAATTTAA
1 TTGCATGATTTAATATATTCGCATGATTATT-ATATGTTATTTACATCAGTTTAATTTAA
*
1699297 TTGCATGATTTATTATAT
1 TTGCATGATTTAATATAT
1699315 AATTTTGCAT
Statistics
Matches: 67, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
56 28 0.42
57 1 0.01
58 3 0.04
59 11 0.16
60 24 0.36
ACGTcount: A:0.31, C:0.06, G:0.10, T:0.52
Consensus pattern (59 bp):
TTGCATGATTTAATATATTCGCATGATTATTATATGTTATTTACATCAGTTTAATTTAA
Found at i:1699270 original size:38 final size:36
Alignment explanation
Indices: 1699142--1699308 Score: 158
Period size: 38 Copynumber: 4.5 Consensus size: 36
1699132 TTGCTTGATG
* *
1699142 TTTACTTGTATGATTTAATATTATTGCATGA-TT-A
1 TTTATTTGCATGATTTAATATTATTGCATGATTTAA
* * *
1699176 TTTGTTTGCATGATTTAATATTATCGCATGATTATTTA
1 TTTATTTGCATGATTTAATATTATTGCATGA-T-TTAA
**
1699214 TTTATTTATATGATTTAATATTATTGCATGATTTAA
1 TTTATTTGCATGATTTAATATTATTGCATGATTTAA
* *
1699250 TATATTTGCATGATTATTAATATGTTATTTGCATCAGTTTAA
1 TTTATTTGCATGA-T-TTAATA--TTA-TTGCATGA-TTTAA
*
1699292 TTTAATTGCATGATTTA
1 TTTATTTGCATGATTTA
1699309 TTATATAATT
Statistics
Matches: 108, Mismatches: 15, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
34 27 0.25
36 13 0.12
37 4 0.04
38 34 0.31
40 6 0.06
41 8 0.07
42 16 0.15
ACGTcount: A:0.30, C:0.06, G:0.11, T:0.53
Consensus pattern (36 bp):
TTTATTTGCATGATTTAATATTATTGCATGATTTAA
Found at i:1699368 original size:25 final size:24
Alignment explanation
Indices: 1699297--1699402 Score: 69
Period size: 25 Copynumber: 4.5 Consensus size: 24
1699287 TTTAATTTAA
*
1699297 TTGCATGATTTATTATAT-A-ATT
1 TTGCATGATTTATTGTATGATATT
* *
1699319 TTGCATGA-TTATT-TTTGGGTGATT
1 TTGCATGATTTATTGTAT-GAT-ATT
1699343 TTGGCATGATTTATTGTATGATATT
1 TT-GCATGATTTATTGTATGATATT
** * *
1699368 TTTTAT-ATTTATTGCATGATGTCT
1 TTGCATGATTTATTGTATGATAT-T
*
1699392 TGGCATGATTT
1 TTGCATGATTT
1699403 TTTATAAAAT
Statistics
Matches: 64, Mismatches: 11, Indels: 15
0.71 0.12 0.17
Matches are distributed among these distances:
20 2 0.03
21 5 0.08
22 8 0.12
23 14 0.22
24 11 0.17
25 15 0.23
26 7 0.11
27 2 0.03
ACGTcount: A:0.23, C:0.06, G:0.18, T:0.54
Consensus pattern (24 bp):
TTGCATGATTTATTGTATGATATT
Found at i:1701367 original size:16 final size:15
Alignment explanation
Indices: 1701346--1701397 Score: 59
Period size: 16 Copynumber: 3.3 Consensus size: 15
1701336 TGGAAACATG
1701346 AAAGAAAAAGAAGAAA
1 AAAGAAAAAGAA-AAA
*
1701362 AAAGAAAAGGAAAAA
1 AAAGAAAAAGAAAAA
* *
1701377 AATGAAAGAAAAAAAA
1 AAAGAAA-AAGAAAAA
1701393 AAAGA
1 AAAGA
1701398 TGAAAATGCA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
15 9 0.30
16 21 0.70
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (15 bp):
AAAGAAAAAGAAAAA
Found at i:1701374 original size:26 final size:26
Alignment explanation
Indices: 1701345--1701396 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
1701335 GTGGAAACAT
*
1701345 GAAAGAAAAAG-AAGAAAAAAGAAAAG
1 GAAA-AAAAAGAAAGAAAAAAAAAAAG
*
1701371 GAAAAAAATGAAAGAAAAAAAAAAAG
1 GAAAAAAAAGAAAGAAAAAAAAAAAG
1701397 ATGAAAATGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 5 0.22
26 18 0.78
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (26 bp):
GAAAAAAAAGAAAGAAAAAAAAAAAG
Found at i:1701386 original size:19 final size:19
Alignment explanation
Indices: 1701362--1701402 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1701352 AAAGAAGAAA
*
1701362 AAAGAAAAGGAAAAAA-ATG
1 AAAGAAAA-AAAAAAAGATG
1701381 AAAGAAAAAAAAAAAGATG
1 AAAGAAAAAAAAAAAGATG
1701400 AAA
1 AAA
1701403 ATGCATGTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (19 bp):
AAAGAAAAAAAAAAAGATG
Found at i:1701387 original size:13 final size:14
Alignment explanation
Indices: 1701346--1701392 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 14
1701336 TGGAAACATG
1701346 AAAGAAAAAGAAGAAA
1 AAAG-AAAAGAA-AAA
1701362 AAAGAAAAGGAAAAA
1 AAAGAAAA-GAAAAA
*
1701377 AATG-AAAGAAAAA
1 AAAGAAAAGAAAAA
1701390 AAA
1 AAA
1701393 AAAGATGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
13 8 0.29
14 3 0.11
15 10 0.36
16 7 0.25
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (14 bp):
AAAGAAAAGAAAAA
Found at i:1701403 original size:26 final size:24
Alignment explanation
Indices: 1701348--1701403 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 24
1701338 GAAACATGAA
*
1701348 AGAAAAAGAAGAAAAAAGAAAAGG
1 AGAAAAAGAAGAAAAAAGAAAAAG
*
1701372 AAAAAAATGAAAGAAAAAA-AAAAAG
1 AGAAAAA-G-AAGAAAAAAGAAAAAG
1701397 ATGAAAA
1 A-GAAAA
1701404 TGCATGTTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
24 6 0.23
25 7 0.27
26 13 0.50
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.04
Consensus pattern (24 bp):
AGAAAAAGAAGAAAAAAGAAAAAG
Found at i:1702419 original size:14 final size:13
Alignment explanation
Indices: 1702392--1702435 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 13
1702382 CAAAAATGCT
1702392 TTGT-TTTGATAA
1 TTGTATTTGATAA
1702404 TTGTATTTGCATAA
1 TTGTATTTG-ATAA
*
1702418 TTGCATTTGTATAA
1 TTGTATTTG-ATAA
1702432 TTGT
1 TTGT
1702436 TTGAGTAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
12 4 0.15
13 4 0.15
14 19 0.70
ACGTcount: A:0.25, C:0.05, G:0.16, T:0.55
Consensus pattern (13 bp):
TTGTATTTGATAA
Found at i:1715050 original size:37 final size:37
Alignment explanation
Indices: 1715002--1715075 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
1714992 CCAAATTAAA
1715002 TAATTTGATATTGTCAATTTTATCCTGAAACACGTAT
1 TAATTTGATATTGTCAATTTTATCCTGAAACACGTAT
1715039 TAATTTGATATTGTCAATTTTATCCTGAAACACGTAT
1 TAATTTGATATTGTCAATTTTATCCTGAAACACGTAT
1715076 CACCTTTCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (37 bp):
TAATTTGATATTGTCAATTTTATCCTGAAACACGTAT
Found at i:1719896 original size:25 final size:27
Alignment explanation
Indices: 1719866--1720026 Score: 107
Period size: 25 Copynumber: 6.3 Consensus size: 27
1719856 ATTTTTACTT
1719866 TTTGCATGAT-TTT-TATGATATTTTA
1 TTTGCATGATATTTATATGATATTTTA
1719891 TTTGCATGATATTTATATGATA--TT-
1 TTTGCATGATATTTATATGATATTTTA
* *
1719915 TTTGCATGAATAATTATAAT-ATATATT-
1 TTTGCATG-ATATTTAT-ATGATATTTTA
* * * *
1719942 TTTACATTATATTTTTCATG-GATTTTA
1 TTTGCATGATATTTAT-ATGATATTTTA
*
1719969 TTTGCATG--ATTTAT-T-ACTATATT-
1 TTTGCATGATATTTATATGA-TATTTTA
*
1719992 TTTGCATGATGTTTATATGA-ATTTTA
1 TTTGCATGATATTTATATGATATTTTA
*
1720018 TTTGTATGA
1 TTTGCATGA
1720027 ATTATTTGTT
Statistics
Matches: 105, Mismatches: 16, Indels: 29
0.70 0.11 0.19
Matches are distributed among these distances:
23 9 0.09
24 12 0.11
25 36 0.34
26 26 0.25
27 22 0.21
ACGTcount: A:0.29, C:0.05, G:0.11, T:0.55
Consensus pattern (27 bp):
TTTGCATGATATTTATATGATATTTTA
Found at i:1720020 original size:49 final size:47
Alignment explanation
Indices: 1719866--1720184 Score: 152
Period size: 49 Copynumber: 6.8 Consensus size: 47
1719856 ATTTTTACTT
*
1719866 TTTGCATGATTT-TTATGATATTTTATTTGCATGATATTTATATGATATT-
1 TTTGCATGATTTATTAT-ATA--TT-TTTGCATGATATTTATATGATTTTA
* * *
1719915 TTTGCATGAATAATTATAATATATATTTTTACATTATATTTTTCATGGATTTTA
1 TTTGCATG-AT--TTAT--TATATATTTTTGCATGATATTTAT-AT-GATTTTA
*
1719969 TTTGCATGATTTATTACTATATTTTTGCATGATGTTTATATGAATTTTA
1 TTTGCATGATTTATTA-TATATTTTTGCATGATATTTATATG-ATTTTA
* * * * *
1720018 TTTGTATGA---ATTATTTGTTTTTGCATG--A-TT-GATGATATTA
1 TTTGCATGATTTATTATATATTTTTGCATGATATTTATATGATTTTA
* * * **
1720058 -TTGCATGA--TATTATTATATTTTTACTTGAT-TTTATTTTGATACT-
1 TTTGCATGATTTATTA-TATATTTTTGCATGATATTTA-TATGATTTTA
* * * *
1720102 TTTGCATGATTTA-T-GATATTATTGCATGAT-TTTATTATAATATT-
1 TTTGCATGATTTATTATATATTTTTGCATGATATTTA-TATGATTTTA
* *
1720146 TTTGTATGACTTTTATTATGATATTATTGCATGATATTT
1 TTTGCATGA--TTTATTAT-ATATTTTTGCATGATATTT
1720185 TTCTATGATA
Statistics
Matches: 212, Mismatches: 31, Indels: 53
0.72 0.10 0.18
Matches are distributed among these distances:
39 7 0.03
40 9 0.04
41 13 0.06
42 2 0.01
43 2 0.01
44 31 0.15
45 26 0.12
46 9 0.04
47 3 0.01
48 1 0.00
49 41 0.19
50 23 0.11
51 17 0.08
52 6 0.03
53 8 0.04
54 11 0.05
55 3 0.01
ACGTcount: A:0.28, C:0.05, G:0.12, T:0.56
Consensus pattern (47 bp):
TTTGCATGATTTATTATATATTTTTGCATGATATTTATATGATTTTA
Found at i:1720062 original size:65 final size:67
Alignment explanation
Indices: 1719987--1720180 Score: 197
Period size: 65 Copynumber: 2.9 Consensus size: 67
1719977 ATTTATTACT
*
1719987 ATATTTTTGCATGATGTTTA-TATGAATTTTATTTGTATGAATTA-TTTG-T-TTTTGCATGATT
1 ATATTATTGCATGAT-TTTATTAT-AATTTTATTTGTATGAATTATTTTGATATTTTGCATGATT
1720048 GATG
64 GATG
* * * * *
1720052 ATATTATTGCATGATATTATTATATTTTTACTTG-AT--TTTATTTTGATACTTTTGCATGATTT
1 ATATTATTGCATGATTTTATTATAATTTTATTTGTATGAATTATTTTGATA-TTTTGCATGATTG
1720114 ATG
65 ATG
* * *
1720117 ATATTATTGCATGATTTTATTATAATATT-TTTGTATGACTTTTATTATGATATTATTGCATGAT
1 ATATTATTGCATGATTTTATTATAATTTTATTTGTATGA--ATTATTTTGATATT-TTGCATGAT
1720181 ATTTTTCTAT
Statistics
Matches: 107, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
61 3 0.03
62 4 0.04
63 3 0.03
64 15 0.14
65 60 0.56
68 2 0.02
69 20 0.19
ACGTcount: A:0.27, C:0.05, G:0.13, T:0.56
Consensus pattern (67 bp):
ATATTATTGCATGATTTTATTATAATTTTATTTGTATGAATTATTTTGATATTTTGCATGATTGA
TG
Found at i:1720063 original size:20 final size:20
Alignment explanation
Indices: 1720038--1720133 Score: 86
Period size: 20 Copynumber: 4.5 Consensus size: 20
1720028 TTATTTGTTT
*
1720038 TTGCATGATTGATGATATTA
1 TTGCATGATTTATGATATTA
* *
1720058 TTGCATGATATTATTATATTT
1 TTGCATGAT-TTATGATATTA
* *
1720079 TTACTTGATTTTATTTTGATACTT-
1 TTGCATGA-TTTA---TGATA-TTA
1720103 TTGCATGATTTATGATATTA
1 TTGCATGATTTATGATATTA
1720123 TTGCATGATTT
1 TTGCATGATTT
1720134 TATTATAATA
Statistics
Matches: 61, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
19 2 0.03
20 25 0.41
21 17 0.28
22 1 0.02
23 4 0.07
24 10 0.16
25 2 0.03
ACGTcount: A:0.26, C:0.06, G:0.14, T:0.54
Consensus pattern (20 bp):
TTGCATGATTTATGATATTA
Found at i:1720130 original size:13 final size:13
Alignment explanation
Indices: 1720114--1720196 Score: 59
Period size: 13 Copynumber: 6.6 Consensus size: 13
1720104 TGCATGATTT
1720114 ATGATATTATTGC
1 ATGATATTATTGC
*
1720127 ATGATTTTATT--
1 ATGATATTATTGC
* * *
1720138 ATAATATTTTTGT
1 ATGATATTATTGC
*
1720151 ATGACTTTTATT--
1 ATGA-TATTATTGC
1720163 ATGATATTATTGC
1 ATGATATTATTGC
*
1720176 ATGATATT-TTTC
1 ATGATATTATTGC
1720188 TATGATATT
1 -ATGATATT
1720197 TTGATTGTAT
Statistics
Matches: 55, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
11 14 0.25
12 7 0.13
13 29 0.53
14 5 0.09
ACGTcount: A:0.29, C:0.05, G:0.11, T:0.55
Consensus pattern (13 bp):
ATGATATTATTGC
Found at i:1720136 original size:44 final size:44
Alignment explanation
Indices: 1720049--1720199 Score: 142
Period size: 44 Copynumber: 3.2 Consensus size: 44
1720039 TGCATGATTG
* * * *
1720049 ATGATATTATTGCATGATATTATTATATTTTTACTTGATTTTATT
1 ATGATATT-TTGCATGATATTATGATATTATTGCATGATTTTATT
*
1720094 TTGATACTTTTGCATGAT-TTATGATATTATTGCATGATTTTATT
1 ATGATA-TTTTGCATGATATTATGATATTATTGCATGATTTTATT
* * *
1720138 ATAATATTTTTGTATGACTTTTATTATGATATTATTGCATGATATTTTTCT
1 ATGATA-TTTTGCATGA----TATTATGATATTATTGCATGAT-TTTAT-T
1720189 ATGATATTTTG
1 ATGATATTTTG
1720200 ATTGTATTTT
Statistics
Matches: 87, Mismatches: 11, Indels: 11
0.80 0.10 0.10
Matches are distributed among these distances:
44 35 0.40
45 14 0.16
46 2 0.02
48 1 0.01
49 20 0.23
50 9 0.10
51 6 0.07
ACGTcount: A:0.27, C:0.05, G:0.11, T:0.56
Consensus pattern (44 bp):
ATGATATTTTGCATGATATTATGATATTATTGCATGATTTTATT
Found at i:1720215 original size:24 final size:26
Alignment explanation
Indices: 1720111--1720216 Score: 98
Period size: 24 Copynumber: 4.3 Consensus size: 26
1720101 TTTTGCATGA
1720111 TTTATGATATTATTGCATG--ATTTT
1 TTTATGATATTATTGCATGATATTTT
* * * * *
1720135 ATTATAATATTTTTGTATGA-CTTTT
1 TTTATGATATTATTGCATGATATTTT
*
1720160 ATTATGATATTATTGCATGATATTTT
1 TTTATGATATTATTGCATGATATTTT
*
1720186 TCTATGATATT-TTG-ATTG-TATTTT
1 TTTATGATATTATTGCA-TGATATTTT
1720210 TTTATGA
1 TTTATGA
1720217 CAAAATTTTG
Statistics
Matches: 67, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
24 28 0.42
25 26 0.39
26 13 0.19
ACGTcount: A:0.26, C:0.04, G:0.11, T:0.58
Consensus pattern (26 bp):
TTTATGATATTATTGCATGATATTTT
Found at i:1720913 original size:44 final size:45
Alignment explanation
Indices: 1720792--1720933 Score: 143
Period size: 44 Copynumber: 3.2 Consensus size: 45
1720782 TTTAATGGTT
* *
1720792 TTTATTTTGTAGTTATTTATTATTTTTCATGTG-CACTAACCCT-TTTG
1 TTTATTTTGTAG--ATTTATGATTTTTCATGTGTC-CTAA-TCTATTTG
1720839 TTTATTTTGTAG-TTTATGATTTTTTC-TGTGTCCTAATCTATTTG
1 TTTATTTTGTAGATTTATGA-TTTTTCATGTGTCCTAATCTATTTG
* *
1720883 TTTATTTTGTAGATTT-TGATTTTACATGTGTACC-AATTTATTTG
1 TTTATTTTGTAGATTTATGATTTTTCATGTGT-CCTAATCTATTTG
*
1720927 ATTATTT
1 TTTATTT
1720934 GGATTGGCAT
Statistics
Matches: 84, Mismatches: 5, Indels: 15
0.81 0.05 0.14
Matches are distributed among these distances:
43 7 0.08
44 53 0.63
45 12 0.14
47 12 0.14
ACGTcount: A:0.20, C:0.09, G:0.12, T:0.59
Consensus pattern (45 bp):
TTTATTTTGTAGATTTATGATTTTTCATGTGTCCTAATCTATTTG
Found at i:1723617 original size:18 final size:18
Alignment explanation
Indices: 1723594--1723720 Score: 62
Period size: 18 Copynumber: 6.4 Consensus size: 18
1723584 GTTTGCTTGT
1723594 ATGATTTAATATTATTGC
1 ATGATTTAATATTATTGC
1723612 ATGATTAGATTTAATATTATTGC
1 ---A-T-GATTTAATATTATTGC
* * *
1723635 ATGA-TTATTTATCAATGC
1 ATGATTTA-ATATTATTGC
*
1723653 CTGATTTAATA-TATTTGC
1 ATGATTTAATATTA-TTGC
1723671 ATGATTATTAATATGTTATTCGC
1 ATGA-T-TTAATA--TTATT-GC
*
1723694 ATGGGTTTAAT-TTAATTGC
1 AT-GATTTAATATT-ATTGC
1723713 ATGATTTA
1 ATGATTTA
1723721 TTATATAATT
Statistics
Matches: 83, Mismatches: 10, Indels: 29
0.68 0.08 0.24
Matches are distributed among these distances:
17 4 0.05
18 25 0.30
19 11 0.13
20 10 0.12
21 1 0.01
22 8 0.10
23 23 0.28
24 1 0.01
ACGTcount: A:0.31, C:0.07, G:0.13, T:0.48
Consensus pattern (18 bp):
ATGATTTAATATTATTGC
Found at i:1723622 original size:23 final size:23
Alignment explanation
Indices: 1723596--1723641 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
1723586 TTGCTTGTAT
1723596 GATTTAATATTATTGCATGATTA
1 GATTTAATATTATTGCATGATTA
1723619 GATTTAATATTATTGCATGATTA
1 GATTTAATATTATTGCATGATTA
1723642 TTTATCAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.48
Consensus pattern (23 bp):
GATTTAATATTATTGCATGATTA
Found at i:1723852 original size:65 final size:66
Alignment explanation
Indices: 1723780--1723909 Score: 199
Period size: 65 Copynumber: 2.0 Consensus size: 66
1723770 GATGTTTTTT
* *
1723780 ATATTTATTGCACGATGTCTTAGCATGATTTTTTATAGAA-TTTTATTGGCATGATATTTGTTAT
1 ATATTTATTGCACGATGTCTTAGCATGATTTTTGATAGAAGTTTTATTAGCATGATATTTGTTAT
1723844 G
66 G
* * * *
1723845 ATATTTATTGCATGATGTCTTGGCATGATTTTTGATAGAAGTTTTATTAGTATGATATTTTTTAT
1 ATATTTATTGCACGATGTCTTAGCATGATTTTTGATAGAAGTTTTATTAGCATGATATTTGTTAT
1723910 ATTTGTATGA
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
65 37 0.64
66 21 0.36
ACGTcount: A:0.26, C:0.06, G:0.17, T:0.51
Consensus pattern (66 bp):
ATATTTATTGCACGATGTCTTAGCATGATTTTTGATAGAAGTTTTATTAGCATGATATTTGTTAT
G
Found at i:1725390 original size:136 final size:134
Alignment explanation
Indices: 1725161--1725408 Score: 304
Period size: 136 Copynumber: 1.8 Consensus size: 134
1725151 TGTGTTGCAG
* * * * *
1725161 ACATATATTTGCATATACATTTTTATTCATGTAAGCATCTTGGTATGTATATTCCTTCATTTTTT
1 ACATATATTTGCATATACATTTTTATTCATGTAAACATCTTGATATGTACATTACTTCATTTATT
* * * *
1725226 TGAAGGCAATCTTTGCATTTGTTGTTTTGTACGTTGTTTTAAATATATTTTTTTTACCATGTATT
66 GGAAGGCAATCTTTGCATTTGTTATTTTGTACATAGTTTTAAATATATTTTTTTTACCATGTATT
1725291 ACAT
131 ACAT
* * *
1725295 ACATGTATTTGCATATACATATTTTTATTCATGTAAACATCTTTATATGTACATTATTTCATTTG
1 ACATATATTTGCATATAC--ATTTTTATTCATGTAAACATCTTGATATGTACATTACTTCATTT-
* *
1725360 ATTGGAA-G-AATCTTTGCCTTT-TTCAATTTTGTACATAGTTTTGAATATA
63 ATTGGAAGGCAATCTTTGCATTTGTT--ATTTTGTACATAGTTTTAAATATA
1725409 AATTCTTGTT
Statistics
Matches: 95, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
134 19 0.20
135 12 0.13
136 59 0.62
137 5 0.05
ACGTcount: A:0.27, C:0.12, G:0.11, T:0.50
Consensus pattern (134 bp):
ACATATATTTGCATATACATTTTTATTCATGTAAACATCTTGATATGTACATTACTTCATTTATT
GGAAGGCAATCTTTGCATTTGTTATTTTGTACATAGTTTTAAATATATTTTTTTTACCATGTATT
ACAT
Found at i:1731408 original size:21 final size:21
Alignment explanation
Indices: 1731384--1731424 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1731374 ATTTTTTGAT
1731384 TTTTTGATT-TTTTTTCCTTTC
1 TTTTT-ATTCTTTTTTCCTTTC
*
1731405 TTTTTTTTCTTTTTTCCTTT
1 TTTTTATTCTTTTTTCCTTT
1731425 TTATGGTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.02, C:0.15, G:0.02, T:0.80
Consensus pattern (21 bp):
TTTTTATTCTTTTTTCCTTTC
Found at i:1733415 original size:15 final size:15
Alignment explanation
Indices: 1733395--1733423 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1733385 CAATATTTTT
1733395 AAAAGAATTAAAATG
1 AAAAGAATTAAAATG
1733410 AAAAGAATTAAAAT
1 AAAAGAATTAAAAT
1733424 TAAATATCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.21
Consensus pattern (15 bp):
AAAAGAATTAAAATG
Found at i:1734615 original size:19 final size:19
Alignment explanation
Indices: 1734591--1734639 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
1734581 GGGCTTGGGT
1734591 TAGATTTAGGGTTAAAGAC
1 TAGATTTAGGGTTAAAGAC
*
1734610 TAGATTTAGGGTTAAAGAT
1 TAGATTTAGGGTTAAAGAC
*
1734629 TAGGTTTAGGG
1 TAGATTTAGGG
1734640 CTTAGGGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.33, C:0.02, G:0.31, T:0.35
Consensus pattern (19 bp):
TAGATTTAGGGTTAAAGAC
Found at i:1734646 original size:7 final size:7
Alignment explanation
Indices: 1734631--1734672 Score: 61
Period size: 7 Copynumber: 6.3 Consensus size: 7
1734621 TTAAAGATTA
1734631 GGTTTAG
1 GGTTTAG
*
1734638 GGCTTAG
1 GGTTTAG
1734645 GGTTT--
1 GGTTTAG
1734650 GGTTTAG
1 GGTTTAG
1734657 GGTTTAG
1 GGTTTAG
1734664 GGTTTAG
1 GGTTTAG
1734671 GG
1 GG
1734673 CTGAGGGTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 5 0.16
7 26 0.84
ACGTcount: A:0.12, C:0.02, G:0.45, T:0.40
Consensus pattern (7 bp):
GGTTTAG
Done.